MusicFox, you really got to the heart of my question.
I have a 300T, which is all-tube, and it has a clipping indicator. This confused me because, like you, I assumed overdriving the amp would result in tube distortion, which I like for certain situations. I'm concerned that the clipping indicator is warning of distortion more than true clipping, but I'm relatively new to tube amps, so I'm not sure how far I can push it before I damage something. Hence, I'm a bit leery to test this theory.
Also, I often play guitar through the 300T, and I think the clipping indicator is psyching me out. Even if it's not the case with bass, wouldn't "clipping" essentially amount to harmless tube-driven distortion when running a guitar through the 300T?