To answer your question, yes. The brain cylinder (and hence, the golem if you're putting it in there) retains its living alignment, as well as any skills it had. Given that it's not effecting mental skill bonuses I have to assume that it retains its mental stats; intelligence, wisdom, charisma are of the brain.
HumbleGamer wrote:Is this an extra feature or the normal way golems are created here in this 2e?Extract Brain is an extra feature. If you want your own golem you just cast a Animate Object ritual of the appropriate level. It will be a standard mindless minion. No brains needed.
Just nitpicking this because we're currently in the Rules Forum, but the Animate Objects ritual doesn't actually let you make golems. It specifically only lets you make animated object-style monsters, things with the "Animated X" naming scheme, it seems.
There is discussion of Golem Manuals in Bestiary 1, but as of yet no official way to make or own one.