It's sometimes the combination of the shoe/boot sole and some sand/grit that can get the abrasion really going.
(I have one pair of neoprene 'creek shoes' with a couple of layers of Aquaseal repairs on the heels...).
If you do a 'butt-first' entry, you can give your shoes a 'swish' in the water - that reduces the amount of sand/muck in the boat.
Some folks put a piece of foam on the hull in the heel area - mostly to help keep feet warm in cold water conditions. The foam will wear away but can be replaced fairly easily.

The suggestion of silica additive is a good one. Dynel lasts a bit longer than glass -part of that may be due to the fact that it soaks up more epoxy and makes a thicker layer.

Anyway, don't think of 'heel rub' as a problem - it shows you are using good, efficient paddling technique, driving with your legs!