Have you considered having your Styles use 0 layer, and placing the resultant C3D Objects on the desired layers?
This is what I want to implement, and then let it grow and evolve progressively.
The thing I see being the issue is a proliferation of layers and/or styles. The Style camp wants to keep layers to a minimum, and the Layer camp wants to keep styles to a minimum.
To start from the outset that each-and-every-single aspect of all potential Styles must be accounted for is unrealistic in a production environment that does not have full-time CAD Admin (where the Admin also has to produce), or hire someone for same which I'm sure you'll get to.
That's me!
Sounds like we're in similar situations; only difference being my two camps are 1) let's implement Civil 3D, and 2) let's stick with using Land Desktop 2005 like vanilla AutoCAD.
The thing is, by definition you're not going to get away from the need for myriad layers. Period. No matter which methodology you go with... The issue ultimately becomes do you make your Styles dependent on said layers or not.
Not sure what discipline you're in, but using a basic pipe network as example....
If you make your pipe Styles dependent on layers, then expect to have additional styles to account for presumably an Existing, Proposed, and Future version of said Style, and in order to change a future pipe to a proposed pipe, you will have to both change the style and move the pipe(s) to the new layer.
Whereas if your pipe's Style is set to 0, then you simply change the pipe to the new layer, and that inherits the appropriate layer properties.
Now, as I mentioned above, you should anticipate progressing to some yet unknown level of complexity... In my real-world projects, my pipe Style's for-plot components are set to 0 layer, and my non-plot components are set to a pre-defined no-plot layer (i.e., O.D. of pipe, etc.), as this is a component that I use for design purposes, but do not need plotted in the resultant hardcopies, PDF, etc.
Hope that makes (more?) sense.