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I believe we're just talking about a convenient tool here. It could be bundled inside rosmake, and it could also be split into a separate tool as well. Some might argue that having all the functionality in one supertool is convenient, but then you'll find others who argue that its better to keep each tool separate, focusing on one job alone. Start worrying about where the functionality is and you'll be riding the wheels and roundabouts instead of getting the job done.

There's a tool there which does exactly what you're looking for. Use eros' rosprotect directly, or copy the script and customise it for yourself (it's quite a simple script). The important thing is getting the job done. This one's not a real show stopper when it comes to using ros and there are probably much higher priorities than doing something which has already been implemented (specially as this will probably be unnecessary with the advent of rosbuild2).