The problem I see with giving military legacy points for simply conquering settlements on homeland is it negates anything special or unique about the exploration age. You still need to have something specific to the age to make it stand out, which right now is the focus on the distant lands. So while I do agree that there should still be some way for a purely homeland civ to gain military legacy, there needs to be some additional condition added on to grant legacy points.
This is where I think another element unique to the exploration age can be brought in, and that's religion. You already get extra military legacy points for converting cities in the distant lands. So a condition could be maybe +1 legacy point for conquering plus converting a settlement in the homelands. This way, there's a bit more incentive to spread your religion to your homeland neighbors not just for gaining relics. It would also model some historical periods tied with the exploration age, like the Crusades, the Islamic expansion into West Africa, and the religious mixing in Southeast Asia during the time.
A small bonus like +1 also keeps the main incentive of the age on settling and colonizing the distant lands, and having the converting condition maintains the more unique ability of the Mongols for just going on a conquest spree in the homelands without other conditions.