You cannot drill tempered glass... so if the bottom is tempered they must have cut the hole then tempered the glass... which I do not think would work... but this is an insignificant detail to the topic of the thread... Anyway 
When I bought a used drilled 90 gal I chose your last option... I covered the holes... simply siliconed a piece of 1/4" plexi over the hole on the inside... It has held together fine in constant use and through several moves for about 4 years...
If you use the sump you could use one pump... then split the output with a T or Y fitting and pump back into both returns...
I can't think of a reason why you wouldn't be able to shut down the overflow/return on one side... provided you plug it so it doesn't leak...
There are dozens of ways to set up your sump. Each one is the best method, for a different goal... you have to decide what you want to get out of your sump before you can decide what is the best way to set it up...
When I bought a used drilled 90 gal I chose your last option... I covered the holes... simply siliconed a piece of 1/4" plexi over the hole on the inside... It has held together fine in constant use and through several moves for about 4 years...
If you use the sump you could use one pump... then split the output with a T or Y fitting and pump back into both returns...
I can't think of a reason why you wouldn't be able to shut down the overflow/return on one side... provided you plug it so it doesn't leak...
There are dozens of ways to set up your sump. Each one is the best method, for a different goal... you have to decide what you want to get out of your sump before you can decide what is the best way to set it up...
