From overlayfs.txt:

Symlinks in /proc/PID/ and /proc/PID/fd which point to a non-directory
object in overlayfs will not contain valid absolute paths, only
relative paths leading up to the filesystem's root. This will be
fixed in the future.

For now, as @sj-i suggested, fallback on reading /proc/<pid>/exe. This will not work for mod_php or other embedded SAPIs.