Food for thought...
My late uncles M-1873 Trapdoor Springfield that best can be described as in relic condition with heavy pitting on nearly all metal surfaces. When the barrel was removed a still intact rust blue was revealed.
This has been the case for many original Kentuckies too. Removing the barrel is one way for researchers to ascertain just what type of finish the original rifle had.
So IMHO the barrel rusting in the stock, even if exposed to a little moisture from time to time is a non issue. Some of these firearms were over 200 years old.
Secondly, does it really matter if it does rust in the stock?
If one has to remove the barrel from a fullstock as a matter of anal retentive routine, I suggest the pins be replaced with keys.
As far as glass bedding, To me that's a sign of poor workmanship. Many smiths use it to repair loose breech fit, in that case it has a purpose but the breech should not be loose in the first place.