Haven't seen a client do it, but I agree they need to amend their plan, not because it is a fringe benefit, but because it needs to be excluded elsewhere if that is what they want to do.
From a payroll/timekeeping side, it seems like it could become a nightmare of epic proportions unless they have a very clean streamlined PTO system with very few edits.
I am not sure I would argue TxFrBnfts, but I would ask the "why do they want to exclude compensation during PTO?" question to see if there is a solution there. Is it because they want to lower their employer match? Do they stop other benefits during PTO (health insurance coverage, life insurance, Workers Comp, STD/LTD)? I suspect all those answers are NO. So why this one?