My take / experience - The Astroberry panels (left hand side browser screen) start the Indiserver on the machine as addressed in the browser( DNS/Hosts or IP). So normally this is a remote machine but can if you start the browser on the remote machine, via say VNC, and input 127.0.0.1 then the Indiserver is started,if using Panels, on the "Local" machine.
OK thats daft i hear you say - well not entirely if you dont use Kstars/Ekos or dont use/load the GUI desktop on the remote machine as this still enables you to start your indiserver with the correct "Astroberry" profile (and connect / start/restart via the left Panel in you browser. Not using the Linux Desktop saves resources if you wish to use something like CCDCIEL or CDC(remotely) which will happily talk to 1 or many Indiservers at the same time.
However if you use Kstars/Ekos then as soon as you choose a profile and connect etc Ekos see's Indiserver is already running hence the message you get so long as the profiles match there shouldn't be a problem and you can answer YES to use the existing Indiserver as Kstars/Ekos should just connect to the drivers already loaded so long as the drivers chosen in the profiles are the same.
Last time I asked Radek I think he said the profiles(Ekos/Astroberry panels) were completely separate but this may have changed.
One could argue rightly,in my view, that it would make more sense,if you are to use Kstars/Ekos on the remote machine via VNC, just to start Indiserver from Kstars/Ekos on the remote machine (the one you are VNC'ing too) and not use Astroberry Panels to select and start a profile/Indiserver.
Radek will correct the assumptions that are incorrect - though most are based on actual usage