I have two packages that each create /usr/bin/ffprobe. One of them is ffmpeg from the Deb Multimedia repository, while the other is ffmbc 0.7-rc5 built from source. The hand-rolled one is business-critical, and we used to just install it from source wherever it was necessary. I can only assume it would clobber the ffmpeg file, and there were never any ill effects.
In theory, it should be acceptable for our ffmbc package to overwrite the file from the ffmpeg package. The drawback there is that an update to ffmpeg will overwrite the ffmbc binary. Is there any easy way to reconcile this?