If I'm not mistaken, OHIP's eligibility depends on your eligibility to apply for permanent residency (not necessarily eligible for PR). I think the PER letter should satisfy exactly that (since the CIO has already found you eligible to apply for PR under MI-4), even with the additional wording that the final decision would still depend on Ottawa (doh)
For OHIP:
I don't think you need to worry when it comes to OHIP, since it clearly states that you need only be eligible to apply for PR rather than being eligible for PR itself (two different things, PER email confirms the former). I think even if you got a booklet from ServiceOntario regarding OHIP, it clearly states that one need not have already received medical request to be eligible, so no problem here (though most likely you would have to appeal).
For local tuition rates though, it may be a bit tricky:
Approval-in-principle, from the CIC website, means:
You can always bring up York University's website, and make your school confirm with the ministry (like I did last year). While the wording did change, theoretically, there is no difference between the new and the old wording, only that the new wording emphasizes that the final decision lies completely on the hand of the visa office in question.
EDIT: back in October, the University of Waterloo sent a university-wide email regarding domestic tuition rates for eligible doctoral students. The beginning of the email went:
I really don't think the new wording changed anything regarding your eligibility.