Alright, I think I got it. :) There seems to be a misunderstanding. ;)
Old WP-Piwik versions provided these ways to use them:
1. Use it as a simple plugin just regarding to one blog - OR - use it as a network plugin: global activated but individual configured.
2. Enable multisite mode by changing a boolean in the plugin's source code and use it as "network activated". Now WP-Piwik was running with a central-managed configuration, called WPMU-Piwik.
These old structure based on old WordPress versions with earlier multisite handling ("WordPress MU"). Because changing the boolean each time the plugin was updated was annoying to everyone using "WPMU-Piwik", I decided to use the new options WordPress provides:
1. You can enable your plugin as a simple plugin in a single blog. Nothing changed.
2. You can add the plugin to your WordPress multisite, activate it on each blog and configure it individually. (Similar to use it as a network plugin without changing the boolean before... just the respective activation comesalong.)
3. You can add the plugin to your WordPress mutlisite, activate it as a "network plugin" and use it with a central-managed configuration. (Like using it as a network plugin before with changing the boolean: "WPMU-Piwik".)
Of course I realized I have to explain this much better - and I will do so to avoid misunderstandings.
Please give me some more details about your mapped domain configuration because I like to replicate and fix this issue.