Yosemite, fastest Mac on the market...
This isn't done in the Render Settings or the Output Module settings. This is done by using the Work area in the comp. If you want two different files from two two different sections of same comp, you'll have to duplicate the original comp, rename the duplicate as you see fit, and adjust the work area accordingly.
As you know,
the Render Settings tab offers different options: Render the work area, the complete comp or a custom Time Span.
In previous versions of after effects , this setting was saved in a template when creating one... But now it does'nt save it anymore. As you are pointing out, it always switches it back to render the work area...
Anyone has a workaround?
I have had to do the very thing you seek on a few occasions, and I have always Duplicated comps and altered work areas. Once you get used to it, it's rather simple.