I know that system wide environment variables can be set by adding entries into
/etc/environment
or
/etc/profile
I fear the solution here is a frustrating one: Don't use environment variables. Instead use a file.
So, instead of setting up /etc/environment with:
SPECIAL_VAR='some/path/I/want/later/'
And calling it with:
$SPECIAL_VAR
Instead, create a file at ~/.yourvars with the content:
SPECIAL_VAR='some/path/I/want/later/'
And source the thing every time you need the variable:
cd `source ~/.yourvars; echo $SPECIAL_VAR`
A hack? Perhaps. But it works.