Want menu and dock to remain visible when youtube fullscreen and Mission control is NOT set to Displays have seperate Spaces
Didn't want to write like 4 comments so here's an answer.

Finally things are starting to make sense. The word fullscreen mixed with Displays have separate spaces option deceived me and kept me in a headspace I couldn't get out off. I was thinking of the OS X fullscreen... We can pretty much forget everything I've said so far.

It is definitely super weird that for you, it is acting the way most people want it to work... and there is seemingly no way to make it work the way it works for you... Yet, here we are. 

Since I super don't have a fix for that issue. I'm going to try and offer a workaround. 



Workaround:

Like I suggested before, maybe the simplest solution would be a chrome extension. I'd actually maybe recommend Floating Player. Basically opens the video in current page in its own window with only the title bar of the gui remaining. 

Then if you resize it to fill  the whole screen (maximize it), you should be good to go. 



Maximizing a window

Since OS X Yosemite, clicking the green ball on the top left puts the application window in Fullscreen mode. You don't want that. To actually just maximize a window, you need to hold down Opt/Alt when clicking it. Or double click the title bar. This unfortunately is a bit of a mixed bag... Some applications, including Chrome, maximizes the window by making it full height, but not full width. So maybe don't use that either.

The best way to maximize a window or manage window position and size is to use third party applications. I'd recommend you try out Moom. It's definitely one of the best ones out there, if not the best one. If you don't want to pay anything, I'd say the next best free window manager app is probably Spectacle.