If the pilots are in reality shouldering the company's own tax, two questions are on my mind:
1- How legal? With or without benefits in Switzerland, I cannot see how one would pay tax and not be able to prove that one has paid them afterwards, unless there is a legitimate original tax certificate from the swiss authorities, otherwise, your only argument will be: "I told you I paid tax!"
2- If the company makes more profit, does it mean that the pilots will pay more tax, regardless of the amount of gross salary?
Many more questions of course, e.g. on how or where to find in the Swiss tax system the calculation it is based on. Each country has a working scale to make adjustments on tax vs income, with all the variables.
At the end of the day, how can you prove the tax you paid?