The way this is put together you can run "wineprefix <program> <arguments>" to allow these symlinks to resolve properly.  The default behavior (no arguments) is to open bash, and this behavior propagates such that applications run within the shell work the same way, a couple examples:

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ehoover@lappy:~$ wineprefix

ehoover@lappy:/??/C:$ echo "TEST" | gpg -c --batch --yes --passphrase "test" --output /??/C:/TEST/test.gpg -

ehoover@lappy:/??/C:$ exit

ehoover@lappy:~$ wineprefix gpg -d /??/C:/TEST/test.gpg
gpg: AES256 encrypted data
gpg: encrypted with 1 passphrase
TEST

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So, the symlinks do work for non-wine processors (when launched with the special LD_PRELOAD).

Also, this is only necessary for within-prefix links - any symlinks targeting outside the prefix would not require any special treatment.

Best,

Erich