Walde, in his Latin Etymological dictionary, suggests that alter 'one (of two)' is a comparative without the -yo- of the positive alius 'another, other'. Other words are alteruter 'one of two, either' and altroversum 'on the other side'. Uter 'which (of the two)' and its sibling neuter 'neither of the two'. The two Latin ins come from the same reconstructed root, but different grades: in 'in' from the full grade *en and in- (privative suffix) from *n. I'm not as sure about the in (intensive prefix) as in inflammo and inclutus.

I tend to think of comparison as somewhat logical (like in set theory), but I like your idea that it could be directional. There's definitely a spatial component to prepositions and adverbs.