it was apparently Fdev said the thargoid story would develop depending on player interaction. so we can make a reasonable assumption that if you shoot them they will be hostile, if we try and trade they may be friendlier and if we ignore them they will either ignore us or keep attempting to make contact until we talk back. otherwise player interaction would not affect them at all if they are intended to be hostile to all humans. why hyperdict and just scan and leave? if they were always going to be enemies to all humanity then two things stick out; first they didnt kill all commanders they interdicted. second they did not attack anything imperial or alliance yet - but then neither of those powers have been strip mining barnacles like the feds.
Unless, of course, FDev are just going to make the Thargoids into another PP-style faction and our "interaction" will simply consist of allowing them into a system unopposed and then, once they gain control of it, human travel within that system will be dangerous, or fighting them in an attempt to retain control of it.
In-universe, I'm not sure what to make of the whole Fed' vs Imp' and Alliance thing.
If this whole "Aegis" thing turns out to be exactly what it seems, if it's only Fed's who've stirred up the hornet's nest you'd wonder why the Imp's and Alliance would feel compelled to get involved in Aegis.
If it gets explained, at all, I suspect it'd be done in lore rather than in-game, with the Imp's and Alliance being revealed to have their own reasons for wanting to oppose the Thargoids.