Do you have any sort of proof that the mescaline is in the base form?
pKa is a measure of how easy or difficult it is for a Nitrogen (or other electron acceptor/donor), such as the one in DMT, to be neutral or charged. At a pH of below the pKa, the atom has a proton (H+) and above it does not. In this case, the pKa of the nitrogen is around 11, so that means at physiological pH, 7, the nitrogen will have an extra hydrogen bound to it's lone pair of electrons, it will be charged because of this and it will be soluble in H2O. As the cytoplasm of most cells is 80% H2O, it would serve that this is where the DMT would be found anyway, unless the plant had some reason to sequester it in some special vesicles or on the cell membrane.
This is why THC is produced on the outside of the plant leaves and other parts. THC is such a damned non-polar bugger that it is very difficult to get it into water and the concentration the plant could maintain inside the cells would be miniscule. So it puts it outside. and thats why hash is hash.
I've cut open a few san pedros and i know the mescaline is not contained in that fatty/waxy/non-polar layer on the surface. This is the only place mescaline would be soluble in it's free-base form. Unless it is held somewhere in the lipid bilayer of the cell membrane, which i seriously doubt it would be in such high concentrations, it must be contained in the cytoplasm and therefore must be charged and therefore be in it's protonated state.
that concludes enthobotanicalchemistry 101 for today, next week we will cover why moon cheese is a rich source of salvinorin analogues.