Can I have lower color bit depth in sample buffer than target framebuffer?
What does that even mean? 


It means that multisampling is resolved.

A multisample framebuffer contains multiple samples for each pixel. The combination of samples represents the color of that pixel. The process of converting from multiple samples to a single color is multisample resolving.

By blitting from a multisampled buffer to a non-multisampled buffer, you are telling OpenGL to resolve each pixel's worth of samples into a single sample. Typically, this is done by adding all the sample values up and dividing by the number of samples, but implementations can take weighted averages or something else, depending on the precise nature of each sample.

Generally speaking, it's best that you let the implementation do its job.


  Is there a way to do it in a cross implementation defined manner?


You can program your own resolution by rendering with a multisample texture to a non-multisampled texture. In the FS, you read each fragment's worth of pixels, doing whatever operation you would like to combine them.

But that's probably not going to be as fast as letting the hardware do the multisample resolve itself.