The rationale behind the limited classes and the fuel and tire limits is to contain costs and attract teams that don't want to spend much money. For what it's worth, limited class cars have won the 25 hours of Thunderhill before, beating cars with unlimited fuel and tires.
The penalty for changing more than one tire is one minute, per each additional tire, in excess of the one allowed. If you elect to change all four tires, that's a three minute penalty.
All penalties, including limited class penalties for tires or fuel violations, are served in the penalty box, on a completely separate stop. You cannot serve your penalty at the conclusion of your pit stop. So it's not worth it.
You are allowed to rotate tires, or change a single tire, but not both.
You are also allowed to change as many tires as you want, in your paddock space, behind the fence. This is the paddock space, not the pit lane, so you'll have to transit all the way around the perimeter of the pits to your paddock, at the paddock speed limit, and back out to the re-entry road. Nobody, enduro or limited class, is permitted to fuel the cars in the paddock once the race has begun.
If this sounds overly restrictive or complicated, you always have the option of switching to an enduro class where there are very nearly no limits.
All of this stuff is in the supps....