When you got rid of the battery tray did you drill the old one off and keep the origional panel just withou the tray or did you get hold of a repair panel with no tray?
Reason I ask is I'm smoothing my bay like yours and relocating the fuse box and battery to the boot but my battery panel is solid underneith bar a small scab so dont want to cut the whole panel off.
my battery tray was absolute mint also we was a bit

taking it out at first due to the shell been so clean

,was quite a few years back now like,but im sure we hacked it out and kept everything underneath,then began to smooth the original panel,so yes i reckon you could drill it out,and you should not have to weld another repair panel in

hope this helps bruv