As Fred reports, the Copyright Office's position is that FECA will not legalize commercial skipping. Their position is that the commercials are separate motion pictures, and thus "skipping the entirety of an ad would go beyond the extent of the bill's authority of making limited portions imperceptible."
This analysis seems a little flawed to me. If the broadcast and commercial are truly independent, skipping the commercials shouldn't be an issue in the first place. The problem with transformative actions like skipping commercials is that the result was an unauthorized derivative work - and it seems to me that's what this bill was intended to address. Why should making an entire work imperceptible be an issue? If you're skipping the whole thing, it's hard to make the argument that it's a derivative work. It's not clear what rights skipping a work in its entirety would infringe.
I think it's fair to assume that they are doing this to classify the whole as a compilation. Nothing wrong with that - after all, one would assume the commercials are already protected. That said, I fail to see how this distinction fundamentally changes the fact that the commercial is still a "limited portion" of the compilation. Section 103 explicitly states that protection in the compilation is "independent of, and does not affect or enlarge the scope, duration, ownership ... of any protection in the preexisting material" - and, generally speaking, collective works receive thin protection. Plus, this also raises the question of whether the requisite originality has been met in the selection and arrangement of the commercials. At the very least, it seems that it would have to be addressed on a case by case basis - not a clear rule that commercial skipping is excluded from this bill.
Does the analysis change if, instead of skipping the commercials at playback, you fail to record them in the first place?