I'm pretty sure that Mesophon retained sold ships in the Era2 era as well. At least, it isn't a very recent change.
Capital/world secession limits appear to be hardcoded at >2 capitals + > 100 worlds for all empires, with even L&O theoretically subject to secession above that limit. In practice secession is less likely for L&O because they get a base 90% secession chance reduction plus stacking adjustments from imperial guards, so in practice it almost never occurs but I believe that hypothetically it could still happen (I don't know what the secession equation is, however).
I believe that you could reduce (but not eliminate) the risk for other doctrines by including secessionAdj: { value:N op:factor } in their Trait declarations and/or by allowing them to build units with secessionAdj values (like my
suggestion here, but this is just decreasing their risk of getting a secession event after hitting the threshold, not moving the threshold itself.
Infantry defection is also hardcoded, nothing in the libraries that I know of will change capture mechanics. I agree that there are big problems with infantry capture right now.
10% allocation to basic infantry is absolutely not a deterrent to mature empires, but it prevents new players and throwaway empires from steamrollering them and it makes T&E consistent with other doctrines in being able to build some form of infantry on capitals. To really keep Mesophon from getting annihilated like in Beta I there would need to be a mechanism either for Mesophon to obtain new hub worlds after game start or for them to retaliate against aggressors.