Rebuilding is always enabled
Converting 1-stackers into 2-stackers is not used in tournaments, but may be useful for those who dislike them
Only 1 Dimension Door when a HeroesWorld ruleset is present; it's unclear why this is needed (not used)
Cartographers, Hill Forts, and Keymasters are always banned when playing with rules. When playing without rules, they are used (in this case, only one checkbox is selected — Mage Guild rebuilding); a single checkbox can be made for playing without rules

Banning Obelisks, always the second stack, and building the second level are set by agreement. It's not worth removing these checkboxes, IMHO