the main rules state the only way blights can get there is from over-running other locations
I don't think they say that.
They say that the Necromancer
cannot enter the Monastery or detect heroes there, and they do say that overflow blights from other locations go to the Monastery, but I don't think they ever say that's the only
way blights can get in. (And in fact, they also say in several places that darkness increases above 30 cause blights to appear in the Monastery.)
On the other hand, the From the Abyss
Rule 27.0 wrote:
Note that the Monastery does not protect against the effects of any darkness cards
If you're sure you read somewhere that overflows are the only way to get blights in the Monastery, please find it for me and I'll see if I can get it fixed for future printings.