If you eliminate the wells or welled fenders, where are you going to put your spare?
On a sedan, roadster, or coupe, mount them on the back. On a pickup, there have been several threads lately on innovative solutions.
I called Berts and they have old fenders that they will cut up a patch panel for you at a good price
Since the vehicle is a pickup, you probably should leave one fender with a well (right side if you want to be able to get in and out easier)
There must be different wells or locations, I've seen some of them allow opening the door all the way, and others that restrict the door opening to about 3/4 of the way.
Your car your money.Unless it was a bad install job on the wells and after the work seen involved doing a good job installing a set of wells, I would be inclined to sell the welled ones and buy a good set of non welled fenders. Pull the irons off and sell as a package. Would also save the time patching the hole in the apron where they came thru.
That's what I'd do also. Seems both parties would come out ahead.