A phone number is PI as long as it is tied to your ID. If you managed to get a SIM that is not in any way tied to your ID - then you are fine. This is assuming that nobody tracks your calls etc... but if you use Tor to register a PM account, then you probably know all the do's and dont's of both Tor and prepaid SIMs. As for the second part - yes and no. Yes, PM cannot answer suggesting to move. No, PM is not to blame for that. As it has been pointed out (in one of other threads about PM) this serves as a (not so high) hurdle for spammers, otherwise PMs free tier will turn into spam machine overnight. And paying customers still have to disclose their identity.
Also, if one values their privacy _that much_ then that person should be able to expend some effort to protect it, and not just make a couple of clicks on the webpage.
I support providers that believe this as well, and act in accordance.
Your model more treats privacy as something to be earned or attained through technical knowledge. No thanks. Journalists and whistleblowers need others looking out for them when no one else will.
If Protonmail doesn't solve this by the time my account is up for renewal, I will not be renewing.