[lugerholsterrepair]

Can a take the magazine apart to examine the interior without damaging the wooden base?
No..This would be foolish IMO. Monkeying with an original magazine will almost always end badly.
I would bet there is nothing wrong with it anyway. Luger rounds fit at a pretty steep angle. My advice is to put away your original wood bottom mag and acquire a MecGar replacement if your intent is to shoot the pistol.
If you are concerned that two different ammunition manufacturers have made their 9MM ammo too long..you should invest in a dial caliper so you can sooth your irrational fears with accurate measurements. This is not the first thought that would come into my head.
You should be able to load 5-6 rounds and cycle them in the pistol by hand to test feed. It seems I should mention here that you should do this at the range as it is live ammunition. Just load the rounds and test fire the pistol..I bet it works.