I have this in my .vimrc and it names the swap files with full path names and percent signs just as you describe:
" Store swap files in fixed location, not current directory.
set dir=~/.vimswap//,/var/tmp//,/tmp//,.
The key is the // at the end of the directories. See this note from :help dir:
- For Unix and Win32, if a directory ends in two path separators
"//"
or"\\", the swap file name will be built from the complete path to
the file with all path separators substituted to percent ‘%’ signs.
This will ensure file name uniqueness in the preserve directory.