I would cook one at a time, takes a bit longer but less risk of burning the bottoms and edges of the muffins. Letting the batter sit for a while before cooking shouldn't be a problem.
The most important thing is the type of oven you have. If you don't have a fan forced oven and your element is on the bottom don't bother with turning them as the heat is inconsistent and uneven (even at the top) and if the oven needs to reheat in that time you can risk burning the bottoms of the muffins.
If you have a fan forced oven and no exposed element you should be fine to swap trays. But like Dee said if you do them one at a time they will be fine And another handy purchase is the 24 muffin hole trays as they are often smaller and can fit into the ovens perfectly.
The most important thing is the type of oven you have. If you don't have a fan forced oven and your element is on the bottom don't bother with turning them as the heat is inconsistent and uneven (even at the top) and if the oven needs to reheat in that time you can risk burning the bottoms of the muffins.
If you have a fan forced oven and no exposed element you should be fine to swap trays. But like Dee said if you do them one at a time they will be fine And another handy purchase is the 24 muffin hole trays as they are often smaller and can fit into the ovens perfectly.
we have a fan forced oven & I always cook big batches of biscuits, cakes etc on all the shelves at the same time....never a prob. I never rotate either. Just pop temp a little lower & watch them.
As for leaving the mixture sit, no worries there either....have done this too not a prob.
It's not a fan-forced oven. When my cheeky little munchkin actually lets me get some stuff done again later today, I'll do them one at a time. I've decided it's cold enough to not really worry about having the oven going for the extra time! If I was baking in Summer I might look into doing things a little differently.
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