Just prior to the Siptah update I finally made the sad decision to turn the purge completely off in my single player game (which really, really sucks). I too was sick of purge waves spawning inside my bases, even though my bases were perfectly accessible and some purges worked just fine in their entirety. Apart from the spawning inside my base which I LOATHE, the purge mechanic is just too buggy generally to enjoy anymore. It used to work so much better a year or so ago.