New substitution models are not incorporated automatically

[rbouckaert]

For examples, the BEASTvntr models for microsatellite data or standard named nucleotide and empirical amino acid models from the substmodels package are ignored. This is because the BEAUti template have an entry

<mergepoint id="sbSubstModelTemplates"/>

instead of

<mergepoint id="substModelTemplates"/>

and uses local substitution models only. I understand this is useful for for clock models, but there should not be a problem for substitution models. Perhaps I am missing something.