Instant Architecture also adds tags with the addition of windows and doors. On both FlexTools and Instant Architecture, it is done for your convenience. You can move the geometry to whatever tags you like. But new additions will also add tags and locate the geometry in the automatic tags.
I have struggled with doors and windows myself. That is a very long discussion, and you could PM me if you care to hear my travel stories.
But my question is, why do you want flanges for any window geometry but for cutaway details?