My SXR had foot holds and on the course they were in fact in the way. I did find advantages to getting my back foot into the wider stance of the hold but ultimately when switching stances regularly I would have preferred to not have them.
Wish that said, I didn't consider removing them. That picture is an awesome turf job and even if I didn't prefer them, I would rock them out until they were a structural issue or at least until the turf needed to be replaced.
Yes, you can remove them. I would look into a set of BOB or RRP holds, that widen the tray but the hold itself can be removed. If you are going to spend money and have a hacked up tray, you might as well be able to benefit from them in some way. The slots can easily be stuffed if you join a stock spec race.
Anyway, Remove the turf with a multi tool and razor, finish by sanding.
Cut out the holds. I would use a cutoff wheel, but you could use a grinder, jig saw or a reciprocating saw if necessary. The 3" metal bit for the dremmel that is used with the router works good too. Cut into the hold, not the hull. You might want to make a few smaller cuts and then work back to the OEM hull.
Once you have the hold cut back to the hull, use a grinder with a flap wheel, or a right angle die grinder with a 2 or 3" sanding disk and grind off all fo the replacement glass until you are down to the OEM hull only.
Fill the void space with foam. You can use 2-part expanding foam. Guide the expansion by putting drop plastic on the hull. Even if you turn the hull on it's side, you will get better results using plastic to control the expansion. Foam expand like a mushroom. Plastic causes it to force itself into void spaces and get more complete expansion with fewer pours. Pink foam works well, but is a lot more work. Also, I can't see the advantages. Above the water line you shouldn't get water infiltration into the expanding foam, but if you ski ever flips over with fuel in it, the pink foam could dissolve.
Trim the foam. My favorite tool for this is tree pruning saw. You can also use a drywall saw, hack saw, sawsall or etc. Trim close, but finish by sanding to the proper shape.
I use 1208 for everything. I would sand the foam a few MM behind where you actually want your new glass and put 2-3 layers of 1208 into the hole like a foot hold install, then continues with 2 layers the cover the entire patch and bond it to the hull. The first later should overlap by 1-2 inches and the second layer should overlap by 2-3 inches.
As a side note, you can actually make a patch off the ski for a better result is the surface is flat. Just layup 3 layers of 1208 on a flat surface, let cure then trim to fit the hole in the hull. Use paper and/or tape to make a pattern of the hull hole to transfer to the repair piece you made. Sand with 80 grit and wipe with acetone before installing your patch onto the ski.
(Side bar: You can make an amazing patch for a flat surface by using a simplified compression mold. Cover your patch with plastic, then put a flat piece of wood on it, and then pile a bunch of cinder blocks on it. Then you will have an increadibly well built patch you can stick into the hole in the hull)
Sand your repair. Use talc or microspheres as a filler mixed with your epoxy to blend in your repair. Turf.
Use 3:1 laminating epoxy for the repair.
Disclaimer. There is no one right way to do the job. Different people will give different opinions on which glass to use, how to patch it, how much overlap, etc. Listen to all of them, consult experts and be prepared to accept responsibility for listening to hacks like me.