Mrs Z got hit that way. I think.
At the end of the day your tax return and the treatment of that by the Revenue is what will determine the correct tax owing. Different treatments can result in timing differences as to when you or the Revenue get the actual money, but the net outcome should be the same (as long as a return is completed).
I think the problem arises when the employer continues paying 100% salary (and expects to get the amount of the benefit cheques paid back) without taking account of the fact that some of it should now be tax free.
For example - you are on €1,000 gross each month and take home €600. Now you get €100 benefit as well. This makes €1,100 gross and €700 take home. Your employer asks for the €100 back and you appear to be back to the old amounts *EXCEPT* that it should now be €900 gross, €570 (or whatever) take home, plus €100 tax free from the benefit making a total of €670, but as above you are now getting only €600.
All washes out in the end, but I just don't understand why employers do it this way except to avoid having to issue two instructions to the payroll department - reduce gross pay at the start and re-instate it at the end.
z