Foamy cakey layer on top of lemon squares
I make my lemon squares the same way and get this top.  I haven't noticed it effects the end result.  I lowered my oven temp a bit to help with it, and it doesn't eliminate it, but it's thin and not overly browned.  And once the powdered sugar is on top, no one is any wiser.

The only way I've seen to not have this is to do a stove top version that's finished in the oven.