I've read through the comments on the various options for simultaneous load / unload etc.
I think it is reasonable that a ship could handle more than one type of replenishment. However, that would have to be in a situation where it had simultaneous access to multiple options. For example, a replenishment ship with both fuel and ordnance could transfer both at the same time but two separate ships (tanker and collier) couldn't deliver to the same ship at the same time. I could create a situation where each replenishment ship within a fleet can order its own priorities and the replenishment ships would know what each of the others was doing (so they would work on different ships). This is not order-based though.
I haven't started looking at other types of logistics facilities yet (for ordnance, supplies, cargo, etc) so there is a lot flexibility in what I could do. For example, perhaps colony ships or freighters need shuttles to load or unload cargo at planets without some form of cargo handling facilities. A cargo station might be the equivalent to the fuel station, with a spaceport able to handle both. Perhaps even a spaceport should have some limits to simultaneous cargo handling. Maybe a space elevator becomes an option at some point, or orbital docking facilities.
The actual ordering mechanics may be an issue, as they aren't really flexible enough to handle multiple options at the moment, except for something like 'unload all', which is simultaneous in VB6 Aurora. Maybe could be expanded to Unload All & Replenish but still not ideal, especially for loading. Perhaps some form of package order, where you have a general catch-all loading order but you can specify numerous options within it (load fuel + cargo + colonists + troops). However, this would be a lot of additional work and I am not sure how often such a complex situation would come up. How often do you have fleets with cargo and colonists and troops, etc.?
I think the best option is probably to keep the major loading orders separate (cargo, colonists, troops) but allow replenishment at the same time as other orders. This could be done by including separate orders (Load Colonists vs Load Colonists & Replenish), or by giving ships options to undergo simultaneous replenishment where possible). Some facilities could handle both (spaceport) while others had to handled sequentially (cargo station, refuelling station). There is a lot of scope for different installations or modules and we would start to see real port-type facilities developing.
Thinking out loud, maybe even remove all the logistics facilities from a population entirely and make them into orbital facilities (including maintenance facilities, fuelling, cargo handling, ordnance replenishment, etc.), which would be created using the ship design process. Essentially once a ship is in space, it stays in space. Anything produced on a planetary surface would be transported into orbit by the orbital facilities or a ship with cargo shuttles ('cargo shuttles' being an abstract element of a ship component designed for orbit/ground interaction). Possibly could have a new type of ship, known as a 'space station', which only has limited armour (or no armour) but has the ability to join with other 'space stations' to form a larger ship (creating a unique class in the process). That way, you could build the orbital facilities over time. Fleets could then interact with the 'space station' (which would have capacity for various types of logistic handling).
Anyway, still considering options