"but what I find intriguing is that by giving Gene the saviour/protector role of child!Alex (which provides an alternate explanation of why she ended up in 1981 - she did in fact have surpressed memories of Gene and the police station)"

Ah, that's an explanation that never occurred to me.

I actually saw it in a completely different light. It made me see the whole series in a 'religious' light. Imagine Gene as the seriously flawed fallen guardian angel seeking redemption. Visualise his presence in her mind/life as a deliberate act by a divine being. Gene has no knowledge of who/what he is, except for that moment when he says "I'll always be there for you".