I have this issue: if/when I make a new character and have to load the profile I made, I have to got into the gw2 settings and turn on the bottom right and left bars and right bar. They should be saving as activated when I save/reload the mod, but they don't.

True, that is because that are blizzard settings we only trigger. So atm this setting only mirrors the blizzard settings and won't save to the profile.