No, your site  is not unghosted after applying a theme. What happens behind the scenes is that the pre-processing that SharePoint and the web server does just grabs stuff from a known virtual directory. It’s all techie stuff but nothing to worry about. I would however recommend against modifying the css  file from inside the virtual directory as it could be shared and/or not necessarily be in the same place after say an update or a reset (very rare but I’ve seen odd things happen where there’s a physical file  and a virtual directory collide, it’s like watching Godzilla vs. King Kong and it’s not pretty).

Use themes  as you see fit. There is one caveat that updating the theme  doesn’t always immediately appear within sites  using that theme. Either the theme has to be re-applied to the site or a reset or restart of the server has to happen (and even then sometimes they’re not updated) so you might want to consider putting in place a small tool to rip through existing sites and reapply the theme if it ever need changing.