my overflow runs over the top as well just as you described. Its really not the end of the world when you flip it over and the holes don't line up.
You could potentially cut another piece that fills the holes in when the piece is flipped.
I haven't actually had to flip my lexan yet, and its been on there for a few months, it does have a bit of a sag to it, but it still sits in place just fine.
When I used thinner Acrylic ( 1/8" i think) I would flip the pieces for a day, once a week, then put them back.
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