If one hole is out of line, it might not be possible to use all four screws to mount the base.
I would put screws in all four holes, and use a precision straight edge against their shanks to check alignment.
If one hole is out, there is essentially no way for you to fix it.
This man knows what he's talking about. Some of the other suggestions are possible but a waste of time and money.
I go through a lot of used firearms with this problem. The one piece base mentioned by the OP is the first part of the solution
I've had most common actions out there with square mount hole problems of one sort or another.
Sometimes, none of them are on center, or only those on one end of the receiver are acceptable, or one hole on each end is acceptable.
Sometimes, it's possible to modify the mounts by drilling different hole positions, transposing those onto the receiver and drilling/tapping new holes. The old holes can be filled with loctite and screws, then filed off and blued. It's all covered by the bases so no unsightly marks.
This is difficult but not impossible with a one piece mount. If you have to take it to a smith to do the job, it's hardly worth the money the smith has to charge for his time, no matter how good his/her work is.
When three out of four holes are OK, just use three mount screws. Hell, it's worked on Model 7 Remingtons, chambered in short magnums for years.
If it's just one hole on each end, depending on the cartridge, I will use JB Weld or Titanium Putty under each end to secure the base in place. The base has now become a part of the rifle but, it will never be an issue again. While doing this, I fill the holes not being used with the same material and often will use the heads of the unused screws as "mock" screws in the blind holes.
There are lots of options open to you if you do the work yourself.
Make sure you follow the instructions for LocTite and JB Weld/Titanium Putty or it will all go to hell when the first round is fired.