I had ProjectName.exe marked with read overlay.
I did a commit and it offered me to update ProjectName.dproj (which i did not ctached at the moment).
I then opened project Source (which was DPR file obviously) and in its history saw nothing.
Then i r-clicked on ProjectName.exe and made Git/Show Log and realized what happened.
Don't know how this can be untangled, to mix config changes into *.dpr files or somehow add those aux files into project manager to saw them separately, yet... Current state is confusing.
PS. when selecting ProjectName.exe in Project Manager, the Object Inspector would show ProjectName.dproj as a selected object.