FWIW, don't ship a release that contains its own autoexec.cfg (or config.cfg), that's kind of a faux pas. :-)
If you don't mind requiring that your release be in its own folder -- which honestly I think is almost always a good idea anyway -- then shipping with your own quake.rc is fine. Several releases use quake.rc to set up their own specific settings. It is usually a big release like Quoth or AD though.
(More about config files at https://tomeofpreach.wordpress.com/2013/09/05/quake-rc-and-being-a-good-citizen/
For just wateralpha, setting the _wateralpha key in your worldspawn might be the best approach these days, so you don't have to worry about any of that config file stuff. That will only work in Quakespasm-ish engines, Mark V, and FTE as far as I know -- I'm dubious about others like qbism Super8, Darkplaces, JoeQuake, etc. So you could still mention the desired wateralpha in your readme.