Can these be set manually now or only automatic as stated in the July 2016 handbook?
Mind you I guess if the nodes are in the alignment zone then they would be ok.
Only automatic. Just make sure the node arrangement is as described, and keep the baseline zone at zero.
OK. So if I want to use Flex I can’t manually hint the rest of the glyph?
I think it doesn’t matter. Flex hints should get added either way, as long as you have the autohint option on when you export.
Do you have an example where it makes a noticeable difference if you have a flex or not?
Not as yet. I’ve not used Flex to date, but it cropped up in a recent conversation. So there may be need for it in the near future. Will keep it in the back of my mind . . . 
I played around with it a bit and there where almost no difference (in Indesign) with or without a flex. And it only works with very specific paths. So it might not that important.
I think I’m with you on that. I’ve been very impressed with the PS hinting results (auto and especially manual).