yes... build it up... or if you have a very strong and steady hand, you could try taking a grinder and knock down the lip of the pipe coming up out of the floor.
Not meaning to minimize your response, but I own a Venture and had this exact same problem.
More than once.
The question I would be asking is why is the scupper pipe now the highest point in that floor.
Its very well possible that the floor has sunk around the scupper pipe and why is that happening?
I have found that those 2 screws you see next to the scupper can allow water into the floor core making it mushy or having a rotted core that may extend quite a ways back into the cockpit.
Or perhaps that line at the front edge is a crack doing the same, or both. And maybe the cockpit/companionway support board below might be missing. Or all of the above.
I had to replace the entire floor because I didn't like how mushy it was along with the scupper problem.
That spot is a super critical support point since it rests right on top of the rear of the keel trunk. It supports the weight of the entire upper works of the boat in the rear center. Just putting resin in there probably won't stop the problem for long.
At a
minimum I would glass in a board with a scupper hole in it UNDER the cockpit, on top of the keel trunk to stiffen the floor back up and restore height if you aren't interested in actually fixing the floor properly (which you can get away with if you don't sail your boat hard like I do).
I reworked the entire area because the factory build of this critical point was so poorly done.
The scupper now goes through glass only and I will not be using those 2 screws to secure the floor.
I will use a different method to keep the cockpit from floating around under stress when I get back to it this spring.
The top of the keel trunk is now flat matching the bottom of the floor and flat rubber gasket.
Some pics for reference.
Pic1: Is your support board in there?
Pic 1: poor factory fit keel trunk/gasket/pipe/floor
Pic3: What it looks like under your scupper
Pic4: Work in progress...