In reference to this issue as it actually is not only Docker related:
oragono/oragono-docker#15
What I would do is change the makecerts command to stop and ask whether it should overwrite, if it finds existing certificates. Then add two params --overwrite (just overwrite the certs) and --dont-overwrite (don't overwrite them, just ignore them if they already exist), and have the dockerfile / startup file use --dont-overwrite.