I actually did a bunch of testing with johnson pumps and using a Y and a T fitting. You absolutely get better flow and quicker fill times in your bags if you just use one pump per bag.
Ideally if you surf a lot or are concerned with weighting the boat from one side to the other then I would add a 5th pump that is connected between the two v drive bags in the back that just pumps water back and forth. If your surfing on one side and want to switch you could easily just flip a switch to move water from one side to the other wile emptying the side your moving water from and filling the side your moving water to. It sounds complicated but between the two back bags you would actually have 3 pumps. I am actually thinking about doing this mod now just because even with the upgraded 4 pump johnson system switching surfers is a total pain in the butt. That mod would absolutely cut the time in half.
Also if your wakeboarding and one side is washed out you could easily just move water from one side to the other to clean it up. Lots of cool stuff you could do.
Im pretty sure I have only had one person ever surf goofy behind my boat, so fast switch out times are no big deal for me. I did get out this weekend and test everything--my under seat bag filled in about 4 minutes, when it was full I started filling the starboard rear bag for a little offset weight-both using the same thru hull, all while the 1100 was filling. for me this worked perfectly as Ive cut down fill time and increased one bag in size.
I did not drill any holes or make any permanent mods to the boat, some future owner may like that