Why haven’t I see plugins using get_file_data to handle retrieving plugin version?

I don’t think it is possible to answer the question directly. I don’t know why you haven’t seen similar code and I don’t know why plugin authors do or don’t use similar code. However…

The functions you mention locate, read, and process a file. It is going to be quicker and easier, both writing the code and (probably) executing it, to use a constant to hold the version number than it is to locate, read, and process a file from the filesystem.

You are correct that this means that there are two version numbers to watch for but I can’t get past the profligacy, in my head anyway, of a plugin reading its own file to find out what version it is. PHP doesn’t compile into an executable so that has to happen on every page load where the version is needed. The details of the implementation could make that a moot point, but in general I would shy away from it.

On the other hand, if a plugin or a theme needed to find data about some other plugin, the functions you mention would be spot on. That is the use case for those functions, in my opinion.