A few errors, and some comments one by one.
So first up I would have a ship with a hanger space of 100k tons, this ship would also have a large amount of maintenance bay parts and so store a huge amount of msp, this should mean two things for me. I can dock ships of 100k tons or less to this base and they will be able to have every possible ship part inside and out repaired while docked, in addition they will also have their maintenance clock reset. All of this would be done using just msp from the base storage and so cost me only the price of msp construction at a colony elsewhere that then needs shipping in whenever the base supplies run low. For arguments sake we will say this base is 1mt in size
You have two options when building maintenance yard after the hangar method, which are planetary PDC and ship based "carriers" (/can be orbital docks or starbases, but that is just fantasy naming, as they are all ships in Auroras functionality).
The thing with building PDC hangars is that those designs are like civil ones and never fail, so you can keep them around forever without raising any costs.
If you decide to have a ship with hangar space like you said above, then you need to understand this ship will also itself be in need of maintenance. This can be okay if you really cut them out to have supply for the decades by making them mostly out of engineering spaces. You just fly or tug them back to some colony then where it can be overhauled, or even better, you have a planetary hangar for this hangar somewhere, so you can fix hangars in hangars.
(Here is a link to
Theodidactus' thread where he seeked out a method to maintain a base in empty systems. I proposed him later there with building such a maintenance hangar somewhere and tugging some modules back for routine inspection at some points.)
There is no way around this, as hangars are otherwise military components.
A needed tip for that though: Be very cautious to have some cheap fallible components on this ship too (for example a size 1 thermal sensor), and do not use any expensive parts (like larger sensors, or high powered engines). Despite rendering a design military, hangars cannot ever get maintenance failures themselves, so a ship entirely consisting of hangars will cause error windows and impede your game. You need a component in there that can actually fail to prevent this, and if you did it right, the component is cheap, and your maintenance life can become...very...veerrryy long. This is because on any 5-day interval only one component per ship can fail at any time, so even if it starts to do that every 5 days, it might still last for nearly forever.(especially if you refill with freighters) Note that Aurora doesn't consider this, so the display on that is actually hugely underestimating the life time in those cases. You will have to calculate per hand (minimum time = MSP_max / most expensive component cost *5 days)
If you follow the link in my signature, you can find a 10mt carrier which nominally only has a couple decades of maintenance life, but since the most expensive part that can fail is still pretty cheap, and a year only has 73 increments, you can easily calculate that this maintenance will last for
at least more than a hundred years even if it should fail every time, which it doesn't of course.(practical experience shows that even after more than 80 years without overhaul it still only fails once per 3-4 increments, and often not the most expensive component, so it is more like 500 years or so
)
So this is actually an alternate method to get pretty much independent mobile carrier ships(/bases), but it is also more bothersome, since you will from then on never quite get rid of those maintenance failure messages in your log. For my game there it is okay, because this and two others are my only long flying military ships anyway, but in my other side game I really don't want this kind of log spam, so I stick to PDC hangars.
Secondly I have another base with enough maintenance modules so that it is capable of supporting ships up to 1mt in size, it would also have recreational facilities, large amounts of fuel storage and a modest amount of msp by way of a few engineering sections. This means the maintenance clock of any ship 1mt in size or less will be frozen when at the same location, and this will use msp from the supply pool of this base?
That is sadly false. Maintenance Modules work exactly like maintenance facilities, so they use minerals instead of MSP. You would need to supply 1/20th of the military hangar's building costs every year in minerals (but nothing of that inside it), and it can only ever be maintained if they stop over a body (planet/asteroid/comet), and only after you dropped said minerals on the ground.
It is quite tedious to do it this way, but I happened to do exactly that two times already.
( it seems conceited to refer to my designs so often, but as lamented above, I am quite literally the only one in Aurora history who has ever cared it seems, and thus the only expert on the matter around. ...Yupp, sounded pretty conceited.
Anyway, here is the link:
http://aurora2.pentarch.org/index.php/topic,6738.0.html )
By keeping these two in the same task group I can just shift msp around to where ever they are needed at any time. The same will be true for fuel meaning any ship/fleet docking at this complex will only be missing two things for unlimited space flight. Firstly will be ammunition if I happen to use missiles, this can easily be solved by adding magazines to the first hanger base. Secondly will be crew morale, this can be fixed by having these two bases positioned at a planet with an empty colony so that the recreational facilities function.
As a little ship operation tip coming from practical experience: When docking a ship on those stations, use the refuel, resupply and rearm commands first, and wait until they are done before ordering the actual docking. 1st reason is because since your repair comes from a ship's inner supply, you would want that filled, and 2nd reason is that I had problems where ships would dock before actually doing the refill orders I gave them before, so do them separately to work out.
And yes, you can add eternally working, safe magazines to any ship by docking a 'magazine'-ship in the hangars.
Quite the nice hack, but is of course less place efficient + you cannot actually fire from those I believe. (..but I never came to actually strain to out to limit the "colliers" option, so maybe this really works)
Anyone spot some black hole in my scheme? I do obviously realise that simply establishing colonies and such could be cheaper/faster/etc but I like the idea of 2,500,000 tons of spinning metal all alone in the night.
Yeah, finally someone. Well, athom too I guess, though I haven't seen evidence yet.
To the colonies: By pure mechanics they are busy work and offer nothing that an automated base cannot do too, except wealth, but that you can normally have in your home system's colonies to any extend desirable, without having so much of the PDC defense demand pressure. I have fallen back to use it for RP issues only anymore, since the bastards grew into multi-billions everywhere in a game, and just kept demanding without giving anything I needed in return.
I quite like colonizing via habitats though, because those populations don't grow and work very efficiently. Great to spread some labs on fortunate spots, or RP inspired starbases around.