Well indeed, the RAW is 1 magical focus, at a time however. So your magus could legally start with certamen as required and then perhaps either buy a different mmf to supersede the House freebie (if you dont mind effectively losing 1 point of Virtues) OR you could have the character initiate a replacement focus during play.
Either way would work within the RAW I would think.
Ghosts would be minor, since spirits, faeries, or magical beats would be major.
I'd say FFM rolls against modified score.
I'd say that a starting Tremere character can certainly start with a magical focus different from the default , since the character either had a preexisting focus to something else, which Tremere training couldn't change (the character can always change the House specialty to Potent Magic) or he underwent an Initiation to develop another kind of magical focus, and sacrifice the House focus as an ordeal during the post-apprenticeship development.