On this one point, the way Scrivener will look in the next release was discussed heavily in this thread. Note that much of the beginning of the discussion is conceptual. If you go to the last few pages, you should find a link to a test program and screenshots of how things will look (I believe this poist is the most up to date)… Due to technical limitations, full hiding will not be available for some time (if ever), but we will be able to fade the intensity of footnote and annotation text to a user customised degree. While they will still occupy the same amount of space on the page, you will be able to diminish their visibility on a sliding scale from pure white (or whatever your paper colour is) to full original appearance.
Oh, and as for spacing out paragraphs automatically. Us MMD users already have to treat Scrivener like a text file. Insert the necessary breaks manually, and make sure that your document joining preferences are set to double break.