well the powroll stroked crank use a shortened rod as well so it is really getting the piston far down at bdc
deciding how much clearance you need and if is safe to remove any at all from the pin boss area is the issue, pics will be needed of the piston
did you have it assembled when you found this out ?
the crank would not need to be turned only remove some material in the correct spot,of course this will change balance rpm's,( a single is not anything like in perfect "balance" only has design "balance" for minimal shaking that is practical at a certain rpm narrow range)it may even be a better spot in the rpm range,that occurs removing the needed metal,may be worse
it may be only a matter of drilling/grinding some material out the opposite side
grinder,drill and scales would be all you need
weigh the assembly,remove needed matrerial on crank under piston at btc
re-weigh crank
remove mo material opposite
its not rocket science,but should be left to somebody with a grip on the entire concept