1- should they have put capping over the parapet?
2- they offered to now put capping on. Will this ruin the membrane.
Hope I’m explaining myself properly.
It is acceptable the way it is or you could install coping over it without compromising the modified.
Personally I would not recommend installing a deck over a roof like that. I would interlocking rubber pavers. If you have a leak or need service they are unlockable and easy to reinstall.
Not seeing any scuppers. If it’s over a heated area, you need to work in a couple vapor vents, too.