Thanks for the update @Francis29029!
As I understand it, mafft --add and mothur align.seqs are using different alignment algorithms so it does not surprise me that you do not obtain the exact same result, but functionally speaking I expected you would arrive at similar deliveries (alignment to a reference alignment).
Thanks for opening your other topic about this; since you are attempting to re-build an existing pipeline with QIIME 2 it makes sense that exact is mission critical for your use case, in which case building a new plugin as you plan to do is a great idea.
Good luck!