if you prop one end of the table up, put it toward the end. I have mine in the corner on all my big tables, then have them all shimmed and leveled to drain towards that corner. Not by much, just enough to drain.
On my smaller veg table, the drain is in the middle
My E&F was tiny compared to Yamaha's but, I too raised one corner and drained from the opposite. At the time I used Rockwool in a bare tub. Any standing water led to algae explosions. I'd imagine a base of hydroton would prevent that.
I'm also inclined (har ahr har) to drill a corner, since DIY trays aren't grooved to drain like their purpose-molded counterparts. Make sure you have plenty of strength and rigidity, like a piece of plywood supporting the tray, so that it cannot sag or even crack under the weight of a flood cycle. Same goes for your reservoir; if you are not using a thick rigid tub, you may need to build a 2x4 exoskeleton to support it.
Shim away, mateys!