Here are some updates to my previous post and some more problems. Win64 v94 now.
Update: somewhere in a decade of turns an officer working at Fleet Intelligence got an increase in Intelligence bonus, so it is possible for officers to have that bonus, but in that decade not a single newly recruited officer arrived with an intelligence bonus.
Update: after that same decade of watching my grav survey ships explode one by one from catastrophic failures I saw my first non-catastrophic failure (an engine) which was repaired from MSP as expected. Even so, I would say there is something wrong with the catastrophic failure frequency.
I see a lot of commanders (scientists and naval officers) get bonuses where instead of the increase being a multiple of 5%, like normal, it's multiple of 5% minus 1%. This leads to scientists who have a 34% bonus to biology, or a naval officer who has a 49% bonus to operations, etc. In Aurora, as far as I know, all bonus increases are either multiples of +5% (normal job) or they are a flat +1% (team member).
There seems to be a problem with the GRAV survey default order. Whenever the game announces that a system has been fully surveyed, if I go check on the system my surveyor will be redoing a survey point that had already been completed. Once it finishes that survey point again it will halt and announce that it can't find any valid survey targets, as expected. This also happens with multiple surveyors working in concert, they will each queue up as their final survey target the survey point that the other vessel is working on, so even after the system is fully surveyed they will run over to the other vessel's survey point and redo it before announcing their failure to find a valid target.
Something similar can happen with GEO surveying but I've only noticed it a few times, possibly because geo surveying a given target is typically very fast. The geo surveyor will queue up the final target twice in a row and survey it twice.
Industries don't stay shut down when turned off in the Civilians & Ind Status tab, the timer starts ticking as soon as you click "shut down" so 180 days later they are back to running again. I'm about to ship my fuel refineries to Venus so they stop using all my Sorium.
Renaming components in the "Design Tech" window doesn't work (or I can't get it to work). The prefix line is editable and works exactly as expected, but when I edit the pregenerated name (e. g. "150 EP Ion Drive" to "Test") my changes aren't reflected in the research topic name after I click "Create", the research topic name just uses the prefix line + pregenerated name.
Adding any hangar module to a vessel changes the displayed "maint life" to 10000. 00 years.
Vessels don't fail their "load [specific installation]" orders when there is none to be loaded. I noticed this after my cargo TG kept on repeating its orders to carry automated mines to Venus years after Earth had run out of automated mines, so the TG was just flying back and forth empty.
Officers don't automatically promote when using manual assignments, and can't be manually promoted.
Jump engine sizes above 100 wrap around to 1, such that selecting an engine size of 105 (the next after 100) creates a size 1 engine.
I don't know if this was a design decision or not but Quasar military/commercial jump engine rules are different from Aurora which goes against your stated goals for the project. In Aurora any vessel with commercial-rated thrusters can jump via a commercial-rated jump drive, regardless of the vessel's overall military/commercial classification, while any vessel of the appropriate size can jump via a military-rated jump drive. In Quasar military vessels can only jump via military-rated drives and commercial vessels can only jump via commercial-rated drives.
This also has in-game implications in that a person might consider using commercial jump drive and engines on a really large military vessel (a carrier or something) in order to avoid researching a really large military jump drive which comes with a huge research cost. Can't do that with the current Q4x mechanics.