Your setup should work, though it looks like there may be some issues with problems plugin. I’m going to try this locally and report back to you how it went.
I can verify that the issue lies in the Problems plugin which has hardcoded folders it looks for. There’s no harm of having those folders even in multi-site setup, so you can either add those back or just keep problems plugin disabled.
Also admin has some hardcoded locations it uses, and I think so has CLI commands, so Ibe careful when using those – or just go ahead and test them out and report any issues back to us!
Yes, I tried to install some plugins with admin interface and it installed in the user/plugins directory instead of the user/site/plugin directory. It’s not that bad have all images, plugins and themes shared between sites, I was thinking if there is a way to just have the pages dir isolated by site, so I can use “themer” plugin to change themes between sites, but also have only one admin for all.