I think/hope I am not alone in having this scenario. I have mass-market clients with subsites which will be funneled to Pro Sites to be managed in terms of features and subscriptions. But I also have legacy custom clients and will continue to have higher-end customers which require custom plans as one-off projects.
These custom subsites in essence will not be included in the Pro Sites pool. I initially thought I would, as I generally have them on a same subscription plan (higher than the highest level in my mass-market plans). But then I realized that my signup page matrix would become more confusing for my mass-market customers.
So now that my custom clients are not part of the mass-market pool managed by Pro Sites, I am seeing that the custom clients still see the "Account/Upgrade" buttons in the top dark grey menu bar when logged in, as well as the Pro Sites upgrade menu on the left in the Dashboard. I am thinking it would be better to not have those displayed for sites that are not part of the pool. Or, if there is a reason for sites to show that, then have another category that will give us the option to not show Pro Sites related UI to specific subsite IDs.
The larger issue that I will need to also resolve is that until know I was using a plugin to disable client (subsite admin) access to the Plugins menu, so they don't mess things up. With the Pro Sites plugin doing its own plugin access management, I will probably need to get rid of that other plugin, which then will enable unfettered access to plugins for all my custom clients with sites that are not part of the Pro Sites pool.
Not sure how to best handle this... any ideas on how to keep my custom clients from having control over plugins which may affect the stability of my whole site network?