Hi emogal,
I cannot confirm that the alignment options would not work; I checked them in MV and they work for me.
However, I can confirm that RS Message Align overrides my plugin's alignment, so when using RS Message Align, you would need to always write \TA[x] for each line. This way, it worked for me.
Remember: In the script box, you need to escape the \ symbol with another \, so instead of
\TA[1]
it's
\\TA[1]
I quickly checked their code but it's unlikely that I will make a patch here given how my and their code is written, I'm afraid.