If you start/stop dovecot with an initscript or some other related
system, you can do what SuSE does, since this problem occurs in lots of
situations, not just dovecot.
Since you know where all the config files are, you could either have the
initscript set up a directory with symlinks, as Timo said, or you could
collect them together and place them all in one file that is in the
correct location. Multiple config files for dovecot can be concatenated
together if you are careful to scan for and accommodate "include"
directives.
Dem