How to Read the Result
The price per user is what to charge so that the margin you chose is left after tooling and labor. The margin is on price, not a markup on cost: a 40% margin on a cost of 60 is a price of 100, not 84.
When Not to Use It
Do not use it for a client whose users are very unequal, like a few power users and many light ones; price those per device or per tier. And check the hours figure against your own ticket data before you quote, because it moves the price more than anything else here.