I'm not an appraiser or a collector, just someone who loves Alembic instruments. For what they may be worth, here are a few thoughts.
It's a beautiful guitar! The inlays, body shape and top and back body laminates make for a unique early Alembic.
An interesting dilemma. From a purely Alembic standpoint, I would imagine that some would want to send the guitar back to Santa Rosa and have it restored. But the Santana aspect kinda complicates that. If it was Santana who made the modifications, then there might be some who would want to leave the guitar as it is.
From the Alembic standpoint, I think it will be useful to know whether the electronics inside the control cavity were modified when the pickups were replaced; and whether all the original parts, including bridge and tailpiece, are in the stash box.
The cost of a restoration would depend significantly on how much of the original parts are missing, especially the electronics, but I'm guessing, would include filling holes and quite possibly doing a complete refinish.
For someone wanting to do a restoration, my guess is that the routing for the tremolo would present a problem. One option might be just to leave the tremolo in place and have the shop make a new back plate. Or even if the tremolo is replaced with an original style bridge and tailpiece, a new plate on the back would probably still be needed.
The routing for the replacement pickups would also present a challenge when mounting original style pickups.
Just focused on the fact that the pickup selector switch has been moved as well.
I'm obviously using the word restoration rather loosely. The wood that was removed for the routing can't be returned to its original appearance.
But I'm also thinking that if the guitar in its present condition was put that way by Santana himself, then I'm guessing there will be those who would want to keep the guitar just the way it is.
An interesting dilemma. And it's exciting to see this guitar turn up. Looking forward to the additional pictures, and of course to seeing what happens with 73-28!