Sorry to revive an old thread, but I have a similar frustration. I’ve been using publish for a while now, and the graph view lacking colorGroups for nodes is very disappointing. I was expecting Publish to sync my graph settings, but my online graph looks extremely monotone and cluttered. On my local vault, I can color the nodes by filename prefixes that I use. But there is no option for this in Publish. (This is one of the big reasons I am looking at competitors to publish now, especial open-source ones)
I understand that plugins are a little too much to ask of publish though. Some of the most popular plugins would put a lot of strain on the server, which would eat into their margins.