"If I spend points for equipment of my Sovereign and later I can give him better equipment in game, am I not gimping him in comparison to someone who only buys stats when creating the Sovereign?"
Interestingly enough that is happening already in the Beta version. Why spend points on a Shield, Sword, Leather Armor and Greaves, when I can pretty much be assured of finding those items on the Map.
One answer is obvious. Until I find them, my SOV is gimped for field use, and if I do not find them at all (unlikely), I cannot go back and add-on researched gear, in game. (something sorely lacking imho) and will change soon surely.
One thing seems a pretty good bet though. The "Super Sovereign" build will be very prominent as well as unavoidable, come early Beta 2 as a non-tweaked Sovereign will surely be the weak link in any proper game start.