the pin hole primitive will give you nice rounded holes when primitives substitution is used,
so dropping them would be a big loss.
i would try to keep them if possible.
you can replace the 1-4ndis corners by ring primitives.
my personal opinion here is that just for getting rid of overlaps you are paying a high price,
i.e., losing primitives substitution, giving you polygonized corners and cylinders.
that price would be too high for me to pay.
the visual loss of polygonized corners and cylinders is so high
in my eyes that is is not worth the gain of getting rid of overlaps.
so dropping them would be a big loss.
i would try to keep them if possible.
you can replace the 1-4ndis corners by ring primitives.
my personal opinion here is that just for getting rid of overlaps you are paying a high price,
i.e., losing primitives substitution, giving you polygonized corners and cylinders.
that price would be too high for me to pay.
the visual loss of polygonized corners and cylinders is so high
in my eyes that is is not worth the gain of getting rid of overlaps.