Sure, like all the rules are recommendation. If it's an explicit rule, it's a hard limit, troupes can always decide to supersede the rules, though. If a character needs to go outside the norm to make something work, then something is wrong, unless everyone at the table has the same opportunity to do something that is forbidden by the rules.
My take on it, the longer I play, is that the limit for Affinity and Puissant exists not to prevent an overpowered character, but to make one who is more complex. Taking 6 of 10 virtues for Affinity and Puissant, even taking the rule limit of 4 is just kinda of meh to me now. To be fair, I've made characters with the 4 virtues in a combo before, but I try and avoid it now, because they aren't as interesting to me.
Unlike Ramidel, I don't consider taking a magical focus to be "magus chargen for dummies." Some things are only possible (especially if starting straight out of gauntlet) with a magical focus. I consider a magical focus as an excuse to specialize (overspecialize?) and I often find characters with it to try and solve all of their problems using their focus. I'm a big fan of specialization, and the only character I've ever made who was a generalist later caused me all kinds of problems, because I didn't like that everyone else could literally do everything he could do, but better. The only virtue I really consider to be a "magus chargen for dummies" is Book Learner; with almost no exceptions magi read to improve their Arts, and many abilities related to the Art. I don't think I've ever made a character with Book Learner.
For a necromancer and a Hermetic shape changer, it makes sense to take a magical focus to resolve the issue you describe, otherwise you end up employing the house rule that it's fine to take more than three affinities with Arts and three Puissant Arts. For the cost of 3-5 virtue points (depends upon focus being major or minor) you can take the Affinity and Puissant Technique, and then spend XP on the Forms to have them in roughly the same range.
But none of this really matters if the saga is configured such that the character you design can quickly get up to speed in that third Art because of the covenant's available texts. The impact of an affinity can be very minor, if high level summa or a vast library of tracts on your preferred Arts exist. Sure, you might gain a season or two when studying a high level summa, over someone without an affinity in the Art, and that can be really useful, but it isn't game altering. And then taking Book Learner is also useful when working in your specialty area and outside of it.
Edited to add:
Also, given the implications of Apprentices and how Hermetic Virtues are passed down I have begun following an unwritten rule for myself of only spending 6 virtue points on Hermetic Virtues (7 if Skilled Parens is in the mix).