Just as a counter balance, I do each filter all the way through including Star Alignment, producing a clean single channel master. Once all of those are complete, I run a second star alignment just on the three masters (either narrowband or RGB). Thereafter no further alignment is necessary, such as when I create a synthetic luminance master (I never shoot luminance subs, which is a whole different discussion). That has never produced any issues for me when I do the extra start alignment, though I guess technically it does involve an extra step. But that is balanced by making it easier to find the various subs I need to complete each channel.
For what it's worth,
Jim