The default values of ENV variables are always stored by Portainer (see portainer/portainer#2952). This causes issues such as endless restart loops when upgrading the container with Portainer. To resolve this issue when upgrading openHAB, first remove all default (non-overridden) ENV variables before starting the new container.
I do not know the original motivation behind that warning, but I can say that it has never impacted me. I’ve been running OH in docker since 3.0 and often use Portainer for quick administration, particularly upgrades. If you have your image set right (most of the time I use openhab/openhab:milestone) then you just need to press the recreate button at the top of the container details page, check the Pull latest image box and set it to go.