Ok got the stand done and some 1/2 inch foam board on top. the outside isn't finished yet as there is still trim and door to do but it will do me for a little bit as it will be changed by spring when I get some oak ply and oak trim for it and finish it as an oak cabinet as the wife doesn't like the walnut finish and I p[refer oak as the lighter color will offset the aquarium better.
I have some 1/4" ply on the top and one thing to remember is it is very flexible so no worries about high spots.
Now let's speak on high spots for a second.
The crown of a piece of dimensional rough lumber is the upward arching curvature you see when you look down its narrowest dimensional edge. so what you want to do for your top wood even the outer edges is to set it so the crowns are all arching downwards. Now most crowns you will notice over a long distance and when we cut down to say 48" you almost wont have any crown but it is good to check and make sure it points downwards.
now for your cross braces yes you can mount them 1/4" lower to be safe but you really dont have to. Look at the below picture this is something we do in the millwright industry when building platforms to make sure there are no High or low points and that everything fits flush.
take your cross brace and clamp or screw it to a board or something stiff like some scrap angle iron.
you then set it in place and tap it down until both sides of your stiff piece is touching the top of your stand. you can then screw it in place and remove your top board. your crosspiece is now perfectly flush with the top of your surface and no need to worry abt a high spot for your aquarium.