Short answer: Yes, EMDM and THEOL are underrated records.
EMDM is one of those albums where I needed to get to a certain point in my life to enjoy. Once I got to that point, I've loved the album ever since. I love it's atmosphere and sincerity. The album flows well and I don't feel that it drags or becomes redundant at any point (like GOAG does). The only song that I'm not totally in love with is "Mutilation..." I feel the song is a little out of place, but not all the time (sometimes it just feels right, it's hard to explain). The title track is one of Manson's best songs, period. It's an album that can certainly be a soundtrack to anyone's life, not just Manson's.
THEOL, technically, may not be as good EMDM, but I have far more emotion invested in it. What it loses for its lack of flow (especially in the middle of the album), it makes up for with its rawness. This is an album I get lost in. Without trying to sound overdramatic, it's an album that kept me going through the darkest time of my short life. The songs: "Devour," "I Want to Kill You Like They Do in the Movies," "I Have to Look Up Just to See Hell," "Into the Fire," and "15" make the album for me. Those songs, coupled with the rest, make for an album experience that I haven't been able to duplicate since. IMO, the flaws make the record better. I don't think this is anywhere near his best record (although, it's far better than what the majority of fans would say), but it's the most important one (to me).