It is very confusing, isn't it. There are so many possiblities but I think only one answers all the clueless.

So throughout the fic Scorpius is crazy from his mothers death, right? He is now using imperio on Draco to make Draco polyjuice as Harry and then fuck, suck and rim him.
creeped out? y/y!


How we know this:
he is brewing polyjuice (boomslag in his closet implied this)
Harry refused his advances and he ignores him at work
the harry the fucks him 'always knows' exactly what he wants and has 'blank eyes'
Draco is 'never around' when harry is around.

So after three reads through and several indepth conversations I'm convince this is what is happening.