After MPRv2 we hoped we could prevent conflicts in git/bitbucket because it was either creating or updating different mxunits. But unfortunately any changes we make even smallest one(changing a button's name) updates the mpr file since mpr file keeps indexes. Therefore we always face conflicts. Does it really need to keep indexes? Can’t mpr file be used only to open projects and read mprcontents folder after Project merged/started so we can avoid changes in mpr file and also conflicts?
Although the conflicts on the MPR file are the symptom you're encountering, the underlying issue is that the Mendix model is expected to be in a valid state (somewhat comparable to not having 'parse errors').
As the Mendix model is split across different files, and these files are expected to always be valid, we do not support operations on the individual files. Using Git for write-actions outside Studio Pro is currently not supported, therefore external tools like Bitbucket / Github / ... also can't do write-actions in a supported way.
To summarize, I think your idea could be rephrased to "support external Git tools for write-actions" or something along those lines. It's a sensible request which we've definitely heard before, but it's also not a trivial thing to do. I can imagine this is something we pick up in the more distant future, but we're not planning for it in the coming year. It'd be quite the undertaking and at this point we're choosing to spend the development resources elsewhere (for example on 'diffing' and 'merge requests within Mendix').