Well, because of the fact that mages actually work well with cyber these days, it's actually a flaw, IMO.
Things like cybereyes, smartlinks, etc(if I recall, mages can only cast spells with augmented vision if it's implanted-remembering this might help), are commonplace even among mages, and these are all affected by this flaw.
Alternately, you can make 2 versions of this flaw-a -10 version and a -20 version. The first being Sensitive System as it is now, the latter the Bio-Rejection, which would leave them out of all non Delta bioware as well. I do believe in SR3, Bio-Rejection allowed you to have things as long as they were grown from your own body. I always thought Delta grade bioware was essentially that, but I could be wrong. In any case, being locked out of everything except Delta-grade Bioware is a pretty big hit.
However, I would not make these flaws worth less for magically active people-for the simple fact that mages/adept with 'ware are actually really, really good. The fact that you can mix and match cyber and bio for less Essence costs also plays in here. (For an example, I had built, for fun, a bio/cyber adept. I wanted to give him Bone Density, but it would have put him beyond 2 points of Essence loss. However, I picked up some bone lacing instead-and since he had less cyber than bio, this was halved, putting him at the 2 essence.)
As for those grevious injury replacement limbs-well, there IS a way around it-but it's it's either rather expensive-or rather gross. The former being them having to get one of their own limbs cloned(and full limbs take awhile and cost quite a bit), the latter being a secondhand natural limb. This wouldn't affect them Essence wise(again, with the flaw as RAW, not the houserule suggestion), but it might be an interesting thing with the party's mage trying to accept someone else's arm who may or may not have agreed with them taking it.
I personally have used this flaw, but I also try to keep within the ''spirit'' of it-Bioware isn't affected, but I've never given one of my characters with this bioware either. I just figured for a character thing-if they were sensitive to one thing, they might not want to take chances with the other thing, etc.