Actually the points of interest inside the dungeons on story mode
don’t count toward the 100% map completion
that awards you with the 2 gifts of exploration,
but…. the points of interest inside the dungeon on explorable
mode count towards the area completions that you see on
the achievement pane and that
once completed give you the title “been there done that”.
So if you want to go for the 100% map completion you don’t need those areas explored, only the hearts, vistas,
pois and skill challenges, but if you want the title you need
the dungeons on explorable mode.
PS: I have the 100% map completion and only 98% of my character
so far towards the achievement because
I haven’t done the explorable dungeons.
Hope this helps