armada2 had an error in its coding resolving the identity of pots which can build stuff by themselves, but i think that should have been fixed in the latest patch. there shouldn't be a problem with identical odfs either. One thing you could check is if your sod does really contain the 3 hardpoints for research yard1, yard2 and yard3.
You could also try to remove the baseName = "byard2" command, a odf with a changed basename is threated like the other odf, so all yards have the same odf from armadas perspective. shouldn't be a problem cause i do also use it in Fleet Operations, but we could try it

yep sadly thats an issue we are still working on. the ai does automatically look for a construction ship to build a base and does not consider research stations. but messing with the AI is a quite difficult thing - but its on the todo

How much AI modification does it look like it will take to integrate all the new Fleet Ops/PP features?

the AI is something very difficult, as far as my knowledge goes DOCa is still working on understanding it just imagine how flexible it is..

well i don't think they wanted to establish this requirement. i'm not much into the programming stuff, but i could imagine that it checks the crafts it commands for function calls, and - perhaps to save time while iterating - it does only check construction rigs. or it does look for constructstation() functions and not for researchpod() functions.. well just guessing here they never needed any different in original Armada2 so they did not need to implement it