I'm also of the opinion shadow meshes should still be included, they are a performance trick even for shadow maps and yes, not all alpha materials should cast shadows but that is obvious. The ability to control shadow mapping on/of per material and or entity should also be a most.
Btw i'm almost afraid to say it, because this is really a radical suggestion... but what would solve many of the problems i'm seeing coming up is...removing stencil shadows all together.
Wait! Don't come with the pitchforks right away! Hear me out ;P ...By doing that, you can then remove noshadow from the materials with no fear of breaking what is not there, and imo logically, removing shadows or not from a object, should be in the hands of the mission maker, not TDM forcing everyone that uses the oficial materials to not have shadows (apart from the obvious ones that should never cast shadows), this way there's no need for a extra keyword either. Anyone wanting to control the shadows, for existing materials per mission, just use a material skin override with noshadow on it, like always, missions where shadow anomalies are detected, because someone faked shadows, should be updated by the mission makers or by a third party if the author is nowhere to be found. Yes this is a radical change indeed but would save many headaches and pretty much all engines i know, use one or the other, supporting two radically different shadow systems in the same game is not easy.
If this is still not the time to think of that then, i may suggest not removing noshadows, let that keyword control only stencil shadows, make another to control shadow maps, that way you don't mess with stencil, for shadow maps, editing the missions at least to remove faked shadows wouldn't be necessary (nor do you want that if playing with stencil shadows), why, because you would only need to stop those particular materials from casting shadow maps and this could be done like i already said, by implementing that new "noshadowmap" keyword on a skin and then just make a script that at map/mission start time would detect the materials you want and swap them.
I can't think of anything better unfortunately.
Because it's not stencil shadows
Yes shadow maps are just textures they do not create extra geometry like stencil does.