koha-plack uses /etc/koha/plack.psgi by default, but it can also use /etc/koha/sites/${instancename}/plack.psgi if one is present. This should be documented in the manpage of koha-plack and the usage embedded in the script.
I could see something like... "koha-plack will start the Plack applications using /etc/koha/sites/${instancename}/plack.psgi if available. Otherwise, it will use /etc/koha/plack.psgi" Maybe something indicating that per-site plack.psgi is for advanced configuration only, and these files will not be automatically updated during upgrades.