I believe it makes zero difference. All of the quickest and fastest jet boats in the world use a pop off valve. The pistons that fill the hand hole opening don't fit super nice, not to mention that most are hideously notched for inducer clearance where the inducer has been moved forward.
That being said, I had a hole in my life that I had to fill with this $10,000 billet hand hole cover.
Blending the hand hole cover void with Bondo or Sea Goin' Poxy Putty will eventually crack and fall out. That chunk then goes through the pump. Sometimes you get lucky and it doesn't cause any damage.
People tend to do what is easiest and hope for some gains. The only way you can know if the bowl is detailed AND if it is done correctly is to look inside. Even if done correctly, that doesn't mean that it didn't suck up some rocks at some point.
If you want to do that, I would build up weld on the hand hole cover, machine it to a 4.250" diameter, and blend the weld to the inside surface of the suction housing.
Roy Miersch, PPP, makes a nice fitting hand hole cover for Berkeley and Dominator pumps.
I don't recommend welding the suction housing, the heat will warp the thrust bearing and wear ring size and alignment.
Have fun,
Joe