Interesting post.
I've restored hundreds of B & M's as well as many other post-war GP's, over the years, and, for what it's worth, here's my take:
They're all the same. Except for the paint job, and a few minor production anomalies such as the color of the coil & armature windings, use of metal coupler "T"s [early production] to the change-over to plastic ones [later production] there's really no structural difference. Therefore, parts of all post-war GP's are completely interchangeable. Re-painting any part, or all of it should not affect the mechanical assembly whatsoever..
Your shell and fame are 100% original Lionel post war parts. From the pix, as best as I can see, your shell still holds it's original paint; the frame may be repainted- But I can't tell with absolute certainty without examining it closer. The riveting job of both the lamp sockets and the battery bracket look they were factory done, or, a pro job using LIONEL factory service tools. Note that the solder lug is still attached to the rear bracket and the rivet roll over on all of them is clean. But in any event, re-painting would not affect or cause the misaligned screw hole.
Most likely your problem is caused by one of two things:
1. When either assembled at the factory, or, even when later repaired, someone cross-threaded the lamp socket's screw thread, forcing the sheet-metal mounting screw in at an angle.
2. The dirt/ or clump pictured in one of your photos may be causing the 'rocking' motion of your shell. Try removing that - carefully- to see if your shell lays flat. Or, the shell really is warped. Could have come from the factory, or stored improperly. It's over 60 years old - so anything's possible!
I don't recommend any major surgery, such as removing the lamp socket and replacing it without proper service tools OR experience. If the frame's paint is still original, and you slip, scratching or damaging it, you've also just lowered the unit's value.
If the shell fits tightly without tightening the screw- leave it. Tighten the screw too much and you'll crack the shell. I've done it, and it's a very expensive lesson.
Good luck to you. If you have further questions, and you'd like to call me, I'll be happy to help you out if I can.
PS: No charge for consultations! LOL!
Len Carparelli
L & L Model Train Restoration Co.