I'm OCD so would replace that tray and the gen vw ones are so cheap and fit like a glove, however if you're not that way inclined you could just trim the rot away, weld in the new corner repair and tack the remaining part of tray to that, a nice bead of seam sealer around the tray and that's job done As long as you get a few good welds along the part of the tray you cut it should be strong enough to support a battery.
Doors are only 1/2" smaller than the opening so that won't work. As LEF says, i'm not inclined to replace the whole tray again as its literally only the width of the back light where the seam sealer had cracked and water had got between the two panels.
I bought a short length of vinyl flooring, folded it and riveted it to the bottom of the doors in a previous garage. Not perfect, but a distinct improvement!
Found part of a deformation panel cut in the shed to use to repair the rotten end of mine. Nice and solid where it needs to be.
Found a little soft spot in the lower corner of the front panel too. Hopefully i won't end up having to replace as much as on the driver's side after i attack it with the angle grinder and cup brush.
I've chopped most of my donor panel up to use. Mostly it was just the bottom where there were no drain holes it had gone and some of the top where someone had screwed (literally using big screws) a couple of spotlights to it.
Spent an afternoon keeping out of the missus' way in the garage welding up crap. Front arch and step are a little more solid now: Unfortunately front beam isn't. It had some wire and filler in it thanks to a PO.
Front panel is battered to hell from having a spare on the front and someone (not me) doing touch parking manouvers. Loads of rot covered in duct tape and some points with filler in it which was bubbling up so i chipped it off. It was 1" thick in places. Thats black go faster duct tape there so its staying put. Actually it covers a hole where the wire used to come out to a car alarm speaker someone mounted behind the spare wheel. I need to rebuild the A pillar bottom (as i did on the driver's side) as its made of filler and booths carrier bags.