Joel, just my $.02 but I'd be tempted to split the difference/mis-alignment on bot the bracket and on the plate. Of course, I have a lathe and milling machine and all the necessary bits and fittings to do that which makes it relatively easy. Alternatively, as Neil said, if you have the room/set-back for the fastener head then you can simply plug weld and re-drill too. Personally, I sort of like a bit of a slot instead.....so I can accommodate some lateral positioning if needed.
Another approach I was thinking about is exchanging these for a set with no holes drilled for the transaxle plate and I’ll line it up and drill the holes myself.