I wouldn't do that. Not yet anyway.
This may have a much simpler solution than is at first apparent. Flint Knapping is not an exact science and the lengths will vary a little from flint to flint.
I buy my flints from Track of the Wolf 10 or 20 at a time, then go through them and pick out the ones for hunting and practice with the rest. When I practice the hammer stall is seldom, if ever, used. But regardless, if the flint edge is not where I want it I go ahead and knap it to where I like it right off.
You could find the shortest "New" flints and give them a try. They might just give you that little extra clearance.
One of my tests for a "hunting" or back up hunting flint is to put it in the jaws and be sure they tighten up properly and the flint sits the way I want it. These go into a dedicated bag and later I may go back through it and pick the best of the best. In a Siler lock a good flint will last for many deer seasons seeing as we seldom take over a few shots a year. I usually take them out and save them at the end of the season for next years hunting.