What does Lame do when it gets (potentially) conflicting command line options? For example, if I say --alt-preset fast standard, but then add -b 96 -mm, are the latter two options ignored? The reason this happens is because I use the Lamer frontend, because it is the only one which runs on my notebook (EAC does not), and allows direct mp3 encoding from line-in.

No, the settings are not ignored. In this case the lowbitrate limit will be 96kbps and it will be mono encoding.

Some switches do not work with --alt-presets though, which wouldn't otherwise be ignored.

As JohnV said, they're not ignored, but make sure you put them in that order. "--alt-preset standard -b 96 -mm" would encode using the standard alt-preset but with a minimum bitrate of 96 kbps and mono encoding, but if you did "-b 96 -mm --alt-preset standard" the -b 128 of --alt-preset would override your -b 96 (not sure about the -mm) and so it would be ignored.