Yes, the restrictions do apply even if you already have a job lined up. In fact, I don't think there is anything forbidding Romanian citizens to look for work for up to three months and they can certainly enter the country without visa, it's only when you want to stay longer than three months or actually need a work permit that the transitory rules kick in. But that does not mean that it's completely impossible to get a permit either.
Specifically, for most EU citizens (and for Romanian and Bulgarian citizens after 2016, if Switzerland does not get out of the agreement until then) the permit is more-or-less a formality (and I think you don't even need to have it before the first day of work, only to apply for it within three months), whereas Romanian citizens need an authorization from day one and can only get it under three conditions:
- No Swiss resident (Swiss citizens and foreigners who are already present in the country) could fill the position
- Work conditions and salary must be approved by the authorities
- Yearly quota is not exhausted
Your employer will therefore need to apply on your behalf to the provincial (“cantonal”) authorities (here is the relevant website for Zürich). I think they will need to publish a job posting through official channels, wait for some time and then submit some information on your job and salary and a motivation letter explaining why they need you. Beyond that, I am not sure exactly what the procedure is.
If that does not work, I can think of a few other solutions to work in Zurich that might or might not apply to your situation:
- Move in with a spouse from another EU country. If your wife or husband is from an EU country other than Romania, Bulgaria or Croatia and finds work in Switzerland (even a part-time poorly paid job could do), he or she could sponsor you for a residence permit that gives you the right to work without restrictions.
- Do the job as a freelance contractor rather than an employee. Restrictions on work permit do not apply to independent contractors but you probably need to have several clients for this to be legal. You also need to show you have sufficient financial means to live in Switzerland without welfare benefits.
- Get hired by a company (possibly a subsidiary of this Israeli company) elsewhere in the EU and then sent to Switzerland as a “posted worker”. It's possible that it would only work for a time (2 years I think) as it's supposed to be for temporary assignments.
All these are wild guesses on my part based on what little I know of EU law and its agreements with Switzerland, I don't know anybody who did any of this and have no idea if it can work in practice so you would need to do additional research and possibly hire a lawyer to find out if it's sensible or not and how to do it. It also requires your prospective employer to be willing to go along with it, which might be a lot to ask for a new recruit.