Hi CPL, Kirk,
Funny you should ask. I was just looking at that. I have exactly five frames in my whole library that have the Exif User field populated. They're from a Canon D30. 37 different Canon models and 23 Nikon models are represented in my library. Apart from that one group of images, nary a single camera or photographer has put anything in that field. So, I would say that it's pretty safe just not to worry about it.
If you want your camera to write your name to the Exif metadata, there is in the menus of most hi-spec modern cameras a place for your name and copyright information. These are written to the Exif Artist and Copyright fields, respectively.
When Photo Mechanic sees a value in those fields, upon committing any metadata edit - clicking "OK", applying a template, whatever - it will copy it to the appropriate IPTC fields, which is where the information actually needs to be. (Most good metadata editing programs do something similar.) When you edit those fields, by, say, applying your standing template to all your images, Photo Mechanic will write the corrected value back to the Exif fields, IF there was a value in those fields in the first place, thus keeping your metadata in sync.
Photo Mechanic Plus will search against the relevant IPTC fields, either a whole bunch of them by default or ones that you specify. It doesn't search those Exif fields. (Nor should it.)
Kirk and all the other developers have had to balance between keeping the data in sync (highly desirable) and whether or not to write into the Exif. (Which nobody is especially anxious to do, given that Exif is essentially logging data.) Different developers have struck different balances. Which makes it important to be mindful when you create a workflow.
All of which brings me back to your original question: how to properly deal with this. My best practices recommendation would be to make sure you get your creator and rights information in the proper IPTC fields by writing it there with your standing Photo Mechanic template. And check to see what your cameras are doing to make sure that the information they write is correct, if not necessarily perfect.
-Carl