So importing the template didn’t work under Wine, and templates and the Linux native version of Scrivener have always been wonky. Here’s a blank project, courtesy of AmberV.
Good luck!
Don’t know if the obfuscation thing works, but there are plenty of perl scripts out there to do the same thing.
nano12_blank.scriv.zip (98.2 KB)
I just had a look at the compile format preset and I don’t think it’s set up to actually do any obfuscation. There should be some basic common letter substitutions in the Preset Replacements tab. That’s all it does, it just swaps e’s for v’s and so on. But the replacement table is empty.
But yeah, that’s always been there for people that don’t know Perl, anyway.
Eh, okay the preset is fine, it’s the Preset Replacements feature itself that is a little buggy.
Ah, glad it’s not just me then. I’ve been using the Nano template with the compile presets .ini file that comes with the Windows Nano 2012 Scrivener version. I tried out the compile and the obfuscation is working fine. However when I tried to compile without the replacements, using a different “format as” target, I still get the replacements.
Yeah, for me the presets didn’t kick in until I went in and out of compile a few times, then after they finally did I couldn’t get rid of them! I don’t know what the deal is there. 
Craaaaaaaaaaaaaaaaap. You weren’t kidding about the compile preset bug.
Found a really nasty bug, too. Don’t try to drag and drop folders from one Scrivener project into another with WINE. Trust me on this, folks.
this is also why rigorous backups are a good thing.