When we did this mod on our Scamp we did not have to disturb that 'sealant'. But I believe it was some sort of silicone...it was solid, not soft like plumbers putty.
On our
Escape, we had to replace the flush valve (we had already put in the cutoff valve). In the
Escape, the supply line was siliconed through a wall from a storage hatch. We had to cut out the silicone and remove the supply line completely to get the toilet out in order to replace the flush valve. When we reinstalled everything, we used some foam (cut off a piece of pipe foam insulation) to fill the gap. Then we secured the pex sections together with a removable elbow fitting (Sharkbite). We figured that if we ever had to replace the toilet (or the flush valve) again the Sharkbite PEX fitting would make it much easier to disconnect that supply line.
Hard to see the black foam stuffed into the hole through the wall but it is there and we have not had any insect issues...but we haven't had that problem anywhere else in the trailer either. It is the dense foam that comes in preformed to fit around a pipe...the circular form made it easier to fill in around the pex in the hole.
We did not do anything to fill in the hole around the Pex that came in from the water supply...just the hole between the hatch and the bathroom.