Missing shader variants/features in asset bundles

From your description, that's exactly what ShaderVariantCollection should do, although I admit I haven't tested it in an assetbundle (though it works for me for shader variants that are swapped in at runtime on a base project)

It might be because "features" are meant to be stripped if they aren't explicitly used in materials. However, "variants" are always generated, since they can be enabled by code. From documentation:

pragma shader_feature is very similar to #pragma multi_compile, the only difference is that unused variants of shader_feature shaders will not be included into game build. So shader_feature makes most sense for keywords that will be set on the materials, while multi_compile for keywords that will be set from code globally.

(There is an exception with fog and lightmap variants since they are stripped if not explicitly used or enabled in graphics settings)

That's definitely the problem, Unity isn't marking the shader features as "in use", but there has to be some way of telling Unity what shader features to include if the shaders are being built into bundles, specially since it works fine if I don't put them into asset bundles.

I'm using too many features to have them be multi_compiled, as the exponential variations of the shader would blow out of proportions and the shaders would become practically un-buildable.