There really are a lot of different categories of MIB encounters, that kid of differ with the time period. Back in the 40's and 50's, they were basically just normal people with military credentials that silenced witnesses using either patriotism, or fear. After that, is when the weird ones come, where they were people, but maybe not exactly human, and the manner of dress, etc. was (by then) a bit antiquated... (and these used primarily fear and intimidation, to silence witnesses and seize evidence). I suspect that these days, we've likely gone back to the model of the 40's and 50's, and just use national security as the justification. Recent MIB cases other than this, are really, really rare. Most of them are far older accounts.
I've spoken a lot with Jenny Randles, probably one of the most passionate researchers on the MIB phenomenon. I don't necessarily agree with her conclusions all the time, but her books are certainly full of research on these cases.