Ok let's take what you have said as a given.
It's all sound and above board.
She is a good friend with a clean record.

She moves in, and from the sounds of it you will see more of her than your SO.
But you get on so that's fine.
Your SO is getting in late cos he is working his *** off.
How do you get time out just the two of you, without having her kind of 3rd wheeling in the background.

Temptation to pour your heart out too her if you and him have any bumps must be avoided at all cost.
Piggy in the middle sux, and always breeds mistrust.

Problems that may occur. She is saving money by staying with you. Before she was just content getting someplace she can afford.
What if in 5 months she comes and says "this is great and everything but if you can give me a couple more months I can get 'this other place.' It's a little dearer, but it's so much better because of a,b&c."

What do you do then?

I am not implying this is malicious in anyway, but boundaries like this are blurry.
She is your friend, you want what's best for her, And hey is this what friends do?
Problem is this is often when friendships get uncomfortable and break up too.

Only can really know what's best for you.
Really hope all works out, either way.