i'll give you an example.
custom payload packets.
by constructing custom payload packets, you are able to send bungeecord plugin messages from skript.
for example, i've made this function before: function sendPluginMessage(player: player, prefix: text, key: text, content: strings).
now, let's say i wanted to send a message to all players on the current proxy i'm connected to. i'd do sendPluginMessage(player, "bungeecord", "main", {_content::*}) {_content::*} = Message,ALL,Message goes here.
of course, the function is pretty complicated as this isn't the easiest way to work with packets, but it's possible. in fact, minehut was so scared of this happening, they removed the addon, and /server commands from player servers.