In some cases it is the free protonated amine that inter-acts with the receptor (no anion but the amine is protonated and thus charged).  I know this is the case with phenethylamines and 5-HT2a but not sure about tryptamines.  Not matter what salt a drug is taken in, this will change once in the body.  If a drug has to be absorbed (it is the freebase that is absorbed.  ALWAYS UNIONIZED) this occurs in the small intestine. 

Once absorbed some may be reprotonated in the blood.  As the freebase distributes more of the protonated form from the blood is converted to freebase, until equilibrium is reached with distribution it is until it is metabolized.  The freebase is the most efficient form for distribution (pharmacokinetics) (transporters aside).  Some molecules may form salts with different anions in the body, it is unlikely to stay with its original anion (pKa's and concentrations considered).  Also a charged molecule dissociates from its anion in solution.  Thus the net charge of the solution maybe neutral but that doesn't mean that protonated DMT has an anion bound to it in solution. Thus what salt was taken does not make a difference.  It is the free protonated form that would interact with the receptor. 

Additionally within a protein there can be specific pH ranges, that can alter the charge on a molecule. For example an amine may become protonated within the receptor itself.  The anion technically being some amino acid residue but the protonated form exists independently of an anion.