There is a difference between a thorough cleaning, (apart, alcohol, ream the cake, etc.) and the normal after the smoke screwing a paper towel into the bowl to smooth the cake and remove excess moisture, and running a pipe cleaner through the stem to remove moisture and clear the draft hole.
However; I don't believe it to be a particularly good thing to create a "strong permanent seal".
There could be taste/souring problems not to mention the possibility of breaking the tenon when you discover that the pipe really needs a good cleaning.
As long as you only remove the stem from the pipe when the pipe is cool/rested you should never have any problem with the stem becoming loose even after years. (That's not to say that it won't happen but with care it shouldn't.)
Just my 2 cents.