Did that really escape you Franken?
No, it did not.
Magazine modification does not affect threading. It is required on some models, if you want to clear a suppressor; but does not impact minimum length or diameter for things like a muzzle brake, unless you're dealing with a Marauder-style rifle with the front barrel band too close to the muzzle to allow threading without moving the barrel band.
Assuming the threading is for a suppressor (as the OP stated):
As you noted, different models have different length magazines. A 336A, 336XLR, or Glenfield Model 30? No magazine modification required. (But moving the sight may be.)
336C, 336W, Glenfield 30A, and many others...? Yea, you're chopping that mag tube. How much depends upon the year of manufacture, and whether or not further work is desirable (or affordable). Barrel lengths have varied slightly over the years, as have magazine tube lengths. Some year/model combinations might only need the mag tube cut far enough to completely remove the old mag tube plug screw hole. Other year/model combinations might require taking as much as 3/4" off, because the mag tube plugs originally extended slightly past the muzzle. And other year/model combinations (such as the Marauders) are going to require chopping enough to appear as a "3/4-length" magazine, in order to remove the barrel band screw slot.
...Unless, of course, the 'smith is going to give you a good deal on TiG welding slots/holes in the existing tube and turning it back to ID and OD to go with the longest length possible. OR, they want to splice magazine tubes and redrill/recut appropriate holes and/or slots.
Who is to say that it's even a Model 336 or Model 30, though? Perhaps the OP is buying a 39A or LeverMatic...
Scorch, will you lose any capacity with the shorter magazine tube? Will you be -1 round in the magazine?
Assuming it's a 336:
Generally, no.
There is usually enough space in the magazine tube, when using a factory spring, mag tube plug, and follower, to cut the mag tube down by as much as an inch without losing capacity or hitting full compression of the spring with the last round fully loaded.
Oh. One last thing:
Guide Guns don't get threaded 1/2-28.