There's not technically any reason the original Catch's discount can't can't apply to Physical Immunity. It's not how the example critter does it...but it could by the rules do precisely that. I think that's idiotic, and would never allow it, but it's technically legal, barring errata.
I do see what you are saying, and I agree. Overall the rules on toughness are actually VERY broke anyway. Example:
Inhuman Toughness -4
Inhuman Recovery -2
The Catch +3
Total cost: -4-2+3 = -3
Human Form +?
Affects Inhuman Recovery ONLY
So is Human Form 0 or +1?
It is clear in this situation though:
Inhuman Recovery -2
The Catch +3
Total cost: -1 (minimum cost)
Human Form +0
Affects Inhuman Recovery ONLY
Then there is this:
Inhuman Toughness -2
Inhuman Recovery -2
The Catch +3
Total cost: -2-2+3 = -1, but there is a -1 minimum cost per power, so it is actually a total cost of -2. However, how do we right this on a character sheet since you don't actually sum these things normally (see the many examples in OW).
All this is really the core problem that Moridens idea is exploiting, and I am dang glad he brought this up because it needs to be fixed in all these variations that people have posted here.