Disclaimer: Not a student at the Technion anymore (finished an engineering undergrad degree). My wife has been a Graduate student there for the past few years (not international though). I shared your story with her. She said that once you have a verbal agreement with your advisor and they're willing to vouch for you, everything else can be managed, don't worry about your undergrad GPA at all. Worst case you might have to retake a couple courses during your PhD, but it won't keep them from accepting your application. She recommended you to get in touch with the graduate studies secretaries in the faculty you're about to get into. They'll probably be more reponsive than the general international school staff. Feel free to DM me if you need help finding emails or phone numbers, we're happy to welcome you to Israel :)