Hi!

You are in an unfortunate situation but what I would advise is the following:
A) do not assume she is trying to mess with you-she is your future employer and you need to start right or it will not work out. These contracts things are complicated and therefore maybe she truly does not know how to handle it.
B) if she knows you will need to work 40 hrs / week then this is what your contract should state and pay reflected accordingly. There is no "minimum wage" in CH but I would say off the top of my head, if you are evry young and inexperienced, it should be still at least 3500/4000 CHF. (This is your gross salary NOT her cost)
C) holidays: she can propose to compensate overtime with holidays, issue is overtime should be exceptional and not regular, there are some rules on this

On the how:
I would suggest setting up a meeting and approaching it more from the standpoint of "having your papers in order". Tell her you really want to do things the legal way and wish for you both to find a solution which is feasible etc etc
Do not accuse her of anything, do not aim to tell her she is wrong. Go with the facts from the authorities and tell her you would like to sort it.

Good luck
K