You can cut the hole and leave a 1/4" gap next to the flange and fill the void with silicone.
Same for the perimeter of the room. Silicone is messy, so if you do the perimeter, begin by masking the floor with painters tape right at the edge of your cut..... then fill the gap full of silicone. Next, use a 1" putty knife to flatten and remove the excess silicone because you don't want the silicone to harden above the floor level which would hold the base or trim from seating against the floor.
Move slow and use a lot of paper towels to wipe the excess silicone from your putty knife as you go. Use a tall paper bag or put an unfolded newspaper in the bathtub to toss each used paper towel. Once you have the gap filled, peel off the tape and put it on that newspaper. You might want to fill and scrape one wall length at a time, but leave the tape on till it's all completed. Be careful with the tape removal so the tape , coated with silicone, doesn't contact the floor.