Kick-tuning technicality question

Often times when working on techno, once I choose a kick drum for a project (which is, at this point, the very first thing that i do) I will then figure out what pitch it is, and then tune it to the key of the track that i want to work with.. usually to the tonic.. next, I'll find that at some point I might "tighten" it up by shortening it's decay in a sampler or maybe transient designer... but, too me, the tune/note of a kick, is oftentimes, that low sub portion, that, once dropping to its lowest point in the decay-phase of it's pitch envelope "peaks-up" at the "root-note" of the kick... Now, after taking that into consideration, if I go and shorten the decay of the kick, then the decay-phase of the kick's pitch-env will be shorter, and thus, will actually be a slightly higher root-note (depending upon how much I shorten the decay)... so this is where my problem/question lies.If I have the kick tuned to G#, and then I short the decay of it, it will then be a little "sharp"... somewhere in between G# and A. It would make sense too me then, to just nudge the kick's tuning in the sampler up a few cents to make up for this change... right? but, sometimes (especially with kick's that have a little saturation on them) the kick will have harmonics present that are related to that bottom freq... which in this case would be related to G#... so, in terms of saturation-caused harmonics, there will be a harmonic that is one-octave higher than the G# sub-tone, and then often times a fifth up from that... so that would be a D#/Eb. Now, since those harmonics actually appear earlier in the kicks envelope-phase, they might not have been changed despite my decreasing of the kicks env-decay... so this leads to a kick-drum that isn't in tune with itself any longer... i.e. the lowest note might now be 5 to 20 cents sharp of G#, but the harmonics G# and D#/Eb may still be the same.So what do some of you guys do in a situation like this?do you:tune the kick up anyway, so that the lowest note is still G# (and therefore in tune to the key your working on), but disregard the upper harmonics which will now be sharp instead.Leave the kick's tune where it is (despite decreasing the decay-envelope), and assume that the kick being sharp 5 - 20 cents+ won't be noticed?Make your own kick elements and just create the sub-layer to be short enough in duration in the first place so that you don't run into any of this crap.Never noticed/considered this phenomenon... and don't care and think, "shut-up dude and go finish a track for once!!"P.S. what does the term "flat" mean in terms of a kick-drum's timbre?