I don't think these need making deeper, they are already very deep
already; much deeper than any of the other doors. It looks as though
someone has ahd trouble with this door before ;(

I did wonder could I fill these in and start again? If I used a two
part epoxy filler, would that take the screws second time round?


Presumably the door closed ok before you took it off, and must do again
if you sort the hinge packing out.
Leave the screws a *little* loose and see if the door will close with
you applying pressure towards the hinge. If so, look at the hinge butt
and you'll see where it wants to sit, and can pack out accordingly.