Yes, I felt the same way, although the author made a nice speech that sold it to me once I had the time to read it... There:
Let tackle this differently, going by your perspective to have a random flaw helping the master, but without the "opening bit".
Rule that there's one (and one only) inherited flaw that, whenever he manifests, counts toward teaching.
The apprentice's gift is weak, he just doesn't do Perdo. It's already there, before the opening, which inflicts no flaw. Yet, when the master tries to teach him his Flawless Magic, he discovers that this is way easier than expected, as the child has a natural gift from it (the ease factor is lessened).
The apprentice's gift is fine, but something goes wrong at the opening. The master later discovers that this shaped the apprentice gift in a way that gives him a natural understanding of Magic.
The apprentice's gift is fine, the opening his fine. Yet, 3 years later, when trying to impart his flawless magic, the master experiments to avoid his Waster of Vis flaw, botches and cripples him, inflicting the Perdo Deficiency.
This accomplishes exactly what you want, but instead of the apprentice having only one possible origin for what may be his hermetic flaw, he now has 3 choices.
Maybe because most masters aren't supposed to transmit a bunch of free virtues, but only 2 or 3, the rest coming from the apprentice's own magic (inherited virtues)?
Also, 21 is to transmit a major virtue without a flaw. It is high especially so that only great teachers will transmit one Free Major Virtue. Without any attached strings. I find it quite reasonnable. Don't you?
So yeah, going by the rules, a Master will only transmit a few virtues, most coming with a flaw. The other virtues and flaws? They are inherited. These high ease factors you're railing against are especially there to keep the apprentices from being their Master's Clone (all their best virtues), with a bunch of added (inherited) virtues.
I also fail to see how you can find fine that a master can transmit his own virtues to his apprentices, but are clearly bothered by his flaws. I mean, it's fine if an apprentice has the same 3 virtues than his master, but not the same 3 flaws?
By the rules, this only concerns a few V/F, it's 2 sides of the same coin. Is it such a great deal if the apprentices has 2 virtues and 2 flaws in common with his master, with 5 that are his own?
It also has its own nice sense of tradition, such as "The Flambeau Lineage of Taake is known for his focus in blood, but aren't very good at Ignem". You're just throwing half of that sentence out.
I understand that, but I like that 
It means that you've gotta make tough choices, instead of just knowing you'll be able to avoid transmitting that hated flaw.
Going by your ruling? Traditions with the most heinous flaws should be almost unknown, since it'll be easier for magi to transmit their Great Secret without their Great Problem. You'll have lineages of magi with Flawless Magic and random flaws, but no lineage of magi with Rigid Magic. IMO, this sucks.
Also, don't forget that masters may have a bunch of flaws to select from. If you really, really, want to avoid that deficiency, give him another flaw, work on your teaching, or... go out! Find another magus to teach him, indebt yourself to him! Go to the magic realm exchange your flaw for another one! Story time! You can already do all that if you really want it. It just shouldn't be easy to give Great Power while Avoiding the mandatory Great Responsability.