Yes, that's a basic fact that I'm well aware of. To hopefully express what I'm saying more clearly: Assume your open strings on a guitar are tuned perfectly in the standard way: the A string is 110 Hz, the low E string is 110 * 2^-5/12 Hz, the D string is 110 * 2^5/12 Hz, and so forth. This will allow you to play an in-tune E minor chord on the open strings, but other chords will not be in tune (again, with reference to the equally-tempered pitch space) to the same degree because of the fact that the strings have different densities and widths. You could imagine accounting for this by tuning the strings such that some other chord was in tune, but then your original E minor chord would no longer be in tune. Thus my point that even though the guitar's design is predicated on equal temperament, it still requires per-key adjustments to be in tune for an arbitrary chord, unless you're using one of the guitars I linked to above.