I suppose the modern sense 'comparative' is too specific. 'Directional', perhaps? That might account for all those direction words like 'inter' and 'dexter' having it. Then there's Latin 'alter', 'uter', English 'other', 'either', etc.

I would have guessed the ma-ter, bhra-ter, pa-ter, dhugha-ter ones were different, maybe agent nouns, related to Latin -tor, and neuter instrument nouns: arator = ploughman, aratrum = plough. But if the experts can connect them, who am I to argue?

The two in-s are only the same in Latin: one's English 'in', Greek 'en', the other's 'un-' and 'a-'. But I know you know that. :)