Yes, I think you're right. I think these songs are concessions (to Iovine, Larry, and possibly just their overriding concern about being "relevant" on a large scale). For all their talk about just playing for the sake of playing together and not worrying about putting an album out, SUC and CT are examples where that is blatantly not the case. Before I go into this, I want to insert the caveat that I think this album is absolutely fantastic, but that I think it is certainly possible to nitpick each of their albums (even the best). I'm not sure if this is nitpicking or not, but here goes: if you listen to SUC on headphones, you quickly realize that this is the exact opposite of MoS. Where MoS is basically live, SUC is a Frankenstein's monster of a song. It sounds like 7 different pieces expertly edited together. The guitar riff is aggressively placed to the front, but somehow sounds clean and, well, unaggressive. The lyrical flow is actually a bit more off-putting than the content, and I can see why Bono kept saying that he was holding the rest of the band back on this song. Plus I think they autotuned Bono's autotuner on some of those high notes in the 2nd half--good gracious it sounds processed. From the descriptions of this song, I thought we were getting something rough and "live"-sounding, but instead we got the most plastic track on the album. U2 would have been better-served pulling an "Eno" and erasing the track and starting from scratch--do a live take with a dirty guitar setting from Edge and then add whatever bits and pieces necessary.
Crazy Tonight is a great pop song in a similar vein to WITS. I really like both of these songs, but I don't think either necessarily fit on an album like this one. CT might be a big single for U2, but I think it should have been a single only. Overall, I think Boots fits well with the rest of the album, but because it is sandwiched between these other two, I can't really tell for sure.
Overall, amazing album that perhaps could have been absolutely phenomenal with two discrete substitutions.