Well from what you wrote, I think it all boil down to a matter of preference : should expansion (military or otherwise) be rewarded with faster research? My answer is no and I would guess that yours is yes. I find that the additional resources, military production and economical base are enough rewards for expansion, and adding faster research just overly favour expansionists nations. It is a game mechanism which actively help winners and obstruct losers (as defined by their size). A bad analogy would be that it's like playing soccer where you would get an extra player for every goal your team score.
Nah you don't understand my point at all. Also, apparently you're not familiar with a concept of conquest in strategy games.
1) In any strategy game i played, conquest was expensive. Depending on specific game mechanics, you lose production so you have less infrastructure, you pay significant unit upkeep so your research suffers, you need to research military techs instead of economy techs and/or you use some other significant resources.
2) If you're on conquest, your army is elsewhere. Like, not in your own cities. Hint: you're vulnerable at that moment.
So, if you commit to a conquest, (1) tells us that your economy suffers as it is, without any additional game mechanics. And (2) tells us that if you attack someone your defense becomes weaker even if you didn't lose any units yet (and you will). In other words, both your economy and military becomes weaker, but you hope to compensate your losses in the future with your newly conquered territory. If you don't get any significant extra research from new territories then your economic research may actually be worse than if you didn't conquer anything at all.
Non-military expansion is very cheap in many games, but military expansion isn't cheap at all. Maybe an extra-early rush is efficient vs AI players (but that's only because of the inferior scouting in TBS genre compared to RTS genre, and overall inferiority of the AI in combat), and even then other neighbours of the victim gain the opportunity to expand cheaply to the victim's land with a non-military expansion and gain free spoils from your costly military expansion (a rush).
So, i agree with you that non-military expansion shouldn't be rewarded too much (like, with extra research). After all, your expansion is limited by a randomly generated map. And if i want randomness to be rewarded, i'll rather play a lottery instead of a strategy game. However, military expansion is costly, risky and isn't that random-dependant so i think it should be rewaded significantly more than a non-military expansion.