Is a paper a statement of personal belief (disagree with PI's writeup)?
It's a tough dynamic and there aren't universal rules. I'm not sure how to answer the original question because 'legitimate' isn't defined and the text rambles.

The central issue remains: how do varying opinions add up to a shared compromising publication in situations of unequal power? That describes almost every collaborative paper. There are many resolutions, including changing your mind based on new information. The bottom line is:

The shared paper requires compromise, and PIs have more power. Some of that asymmetry is appropriate and helpful to junior colleagues in the long-term. Some is not. If you're not comfortable adding your name to the best compromise you can find, then take yourself off the paper or don't publish it.

Also see: Can co-authors disagree in their own paper?