What does "counting" against "notional salary" mean?

Different kinds of expenses (benefits and salaries are expenses) have different tax consequences. Things that are on the pay stub may be taxed differently than things that aren't but I don't think that you're going there.

Are you thinking that telling employees "here's how much I'm spending on you that doesn't appear on your pay-stub" is going to have some effect? If so, I suspect that you're about to learn that some folks would rather have that money in their paycheck and that most will tune you out.