I’m trying to export LaTeX, via Compile, and whatever I enter as name, I get a folder with .tex in the name. I have images, so Scrivener exports a folder; but where previously I could call it “t” and get t/, I now get t.tex/. If I uncheck the “Hide Extension” button, I still get .tex; if I try to delete it in the text box, by the time I get to the dot, I get “Hide Extension” checked again and .tex implicitly there!
Can you guys reproduce it? Any document with a figure in Research linked from Draft will do, with MMD->LaTeX export. E.g. if I have a document “t”, it calls the folder “t.tex” and inside it there’s a “t.tex”. There’s no way to enter anything without t.tex into the text box. 1.0 created t/t.tex structure. Folder names should not have extensions, this is meaningless on Mac OSX and dangerous on other inferior OSes. 
I’m afraid I don’t understand the problem here. I wouldn’t call this a bug, that’s just how it is. It doesn’t hurt anything, and it makes it easier to maintain simultaneous exports of other formats. You can have “t.md”, “t.tex”, and “t.html” going on, and know what is going to be in each folder just by looking at them. If they all just used “t” then they would overwrite each other and create more management hassle for you, having to browse around instead of just hitting the compile button.
As for being dangerous… on what operating system? The only OS I know of that actually turns a folder into a “file” via its extension is none other than the Mac OS. That’s all a .scriv folder is. Try changing the extension on that to .scri and you’ll see it’s just a folder. Change it back to .scriv and now its a “package”. None of the other major OSes out there do anything like that at all, they don’t care one bit if the folder name has a dot in it that may or may not resemble an extension.