I use some scripts to update my plugins on my servers, there is a pluginlist where you can remove plugins you dont want.
I just tested it locally in my single player where i usually not play or test any plugins. i removed some old java plugins from my plugins folder and installed all plugins through my script.
Then i startred a new world in sp and everything worked withput problem, even global intercom worked as expected
I run it from wsl2 using ./download-multiple-plugins.sh pluginlist Plugins --flat --remove-zips
while scripts are in the root game dir.