Just like any other legal or quasi-legal process, the grounds for appeal may be on the inadequate application of the process just as easily as on the evidence. Patently, Bruyneel has no grounds for appeal on the evidence, but as the Arbitration Panrel have expressed their reservations about USADA's handling of the process, specifically confidentiality, he may well have grounds to have the judgement overturned (either through CAS or through the civil courts) on the technical issue of the compromise of his right to a fair trial.
I would be very surprised if any court found that evidence trumps process. We regularly complain here when drivers are let off having KSId cyclists, or in general law, when the patently guilty are not convicted because of some failure of process. That could well be the case here; it doesn't matter how good the evidence is, if it can be shown that a fair trial was impossible due to USADA's lack of confidentiality, the conviction is unsound and will not stand (or wouldn't under criminal law).