Then why is the grave of our Prophet :saw: and his companions Abu Bakr 
and ‘Umar incorporated into Masjid-e-Nabawi, which is a place of worship?
If building over them is prohibited then why do we have a green dome above and a fancy mesh barrier around the graves I mentioned earlier?
I thought we didn’t have any ‘shrines’ in Islam except for the Ka’bah?
The graves weren't originally inside the mosque... subsequent extensions to the mosque over centuries caused the graves to come inside the mosque...
Even if there was an argument for redesigning the mosque so the graves once again fell outside of it as they originally were, the lack of understanding on the part of probably most Muslims about the issue might cause more harm/turmoil than good... there is a precedent from the time of the Prophet (saw) when he wanted to rebuild the Kabah upon its original foundations but desisted because the people had newly entered Islam (i.e. they might not have appreciated or fathomed the need for it etc.)
Re: The Prophet’s (saw) grave
as the brother has rightly replied, the graves were not originally IN the mosque but later became inside…
the fence is there to separate the graves from the mosque so no one will take the graves as shrine(s)…
there is no building on the graves…
they r left in the same condition as they were…
there r ppl (employed staff) in the mosque to keep ignorant ppl from doing any sort of ‘shirk’ acts around the graves…