Ah, thanks for flagging this. You definitely shouldn't be locked out of customizing your option until all the game option upgrades have been maxed. I will fix this in the next release. The first prestige is still pretty messed up in this version of the release.
The prestiges will not actually speed up play as they do in conventional idle games. Maybe prestige isn't the right choice of word. Each "prestige" is intended to unlock a new game option and increase the difficulty of the game. May reconsider the naming.
Thanks for playing!