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I've tested it with research reinvented and it works just fine, haven't tested it with other research mods though. The items in this mod are programmed to simply complete a research project, so as long as those aren't removed by a mod it should be compatible in theory. When in doubt, you can always backup your save file and try it.
Originally my reasoning was that I don't want to create a system that is simply more powerful than vanilla research, but rather to offer a weaker alternative that fits better into certain playstyles. The goal was to enable these playstyles without making them optimal. That is why I wanted to balance this mod rather conservatively.
In hindsight, and considering how many mods add new research projects, some of which are trash tier in most playthroughs, I decided to go with your idea to make it finish the selected project first, if it is of the appropriate tech level or lower. If that doesn't work then the previous random method will be used instead.
As for retro-engineering, a mod called "research reinvented" already does that. It doesn't remove the need for sitting in a room entirely, but it does offer some new ways of doing it, including reverse engineering: https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=2868392160&searchtext=research+reinvented
If you could pick the research (limited by tier), or if it auto-completed whatever research is currently being worked on, that would have been more useful. The first solution would likely be quite the headache though, as it would require a UI portion of some sort.
Being able to retro-engineer items from loot would also make sense, if it counted for a portion of research.
Because base generation expanded handles loot different from the vanilla base generation. So the code that adds the research items to the loot tables isn't going to work if that mod isn't loaded first.
If you know xpath then you can remove that dependency for yourself by removing that part of the patch in the mod files, but then these items won't show up as loot in bases anymore.
Just did some initial testing and these mods seem to work just fine together