Indeed, but that was not the question at hand: "when a judge tells the jury to assume something, is he implying there is a good chance that that is how he would judge the case?"
I guess by your reasoning, then yes, he is implying that, otherwise the implication is always true and there's no logic to assuming a false P.
Thus: I fear for the worst. API's may be copyrightable according to this ruling. I assume Google's teams are all over this right this minute.
P = APICopyrightable
Q = APICopied # infringingly
There are two separate questions being asked here:
1. Is P true?
2. If P is true, does Q follow?
To answer (2), the jury must assume P then evaluate the consequence on Q; that is simply the manner of establishing the validity of a material implication. As you note, if the jury did not assume P, then they would have nothing to do. However, that the judge instructed the jury as such does not indicate any bias on his part; he was simply providing instructions to simplify the procedure of logical reasoning to a group of 12 laypeople. I'm assuming that most of them aren't trained mathematicians, logicians, lawyers, or philosophers.
To put it succintly: the answer to your original question is "No."