Since someone brought up the topic of MPDGs a little while ago, I clicked on this.
Eh, Clementine shouldn't be included, even though she always is with regards to this subject (and I knew she would be) because she looks the part. The thing about her, though, is that she's a subversion, if you can say that about one of the so-called earliest examples of this trope.
She straight up tells Joel what her deal is in their first(?) meeting in the bookstore and, of course, Joel overlooks the warning. In the beginning of the loop, he's seeing her as an MPDG, and as things progress, things become strained as he finds out that's not really a thing. This wouldn't happen if she was actually an MPDG; none of these relationships with MPDGs typically show the gaping fissures we see in this movie. You also have to keep in mind how the movie is about how our memories and perceptions can be flawed and curious things; I think a distinction can be made between how Joel sees her in the beginning and how she is within the broader universe of the film. The movie (unlike Garden State or, I presume, Elizabethtown) was not simply written as a comedy or romance written to appeal to men, like a lot of these other films. There's at least one other level to it; the movie is examining things like memory and desires and how they affect our behavior.
Everybody forgets about this scene, although there's the element to add here that this is filtered through his own perceptions and memories, which might trip people up. He's the one filling in her dialogue; portions of this is his idealization of her and we don't know what the real Clementine thinks because we don't watch her as she undergoes the procedure. This is through Joel's eyes as he undergoes the procedure, but he's an unreliable narrator like all of us are.
TLDR: Clementine is an MPDG within the universe of Joel's mind, but not within the "real world" of the film itself. This is obscured by the fact that this movie is very interested in depicting the contents of Joel's mind.