Hi,
This is an interesting topic and I have already waited for someone to mention it 
.
A Matomo script from a different domain is per definition a 3rd Party Tracking Script.
But the real question is: Will Matomo be blocked?
Firefox’ tracking protection works by comparing the domain of the 3rd party script with the blocklist of disconnect.me:
https://github.com/disconnectme/disconnect-tracking-protection/blob/master/services.json
Or more precisely they run the following script which modifies the list a bit:
So as long as your domain is not on a blocking list for tracking, your Matomo will continue as before.
You can already try it out by enabling tracking protection in the latest firefox version.
Fun Fact: Matomo tracking on http://virtual-drums.com/ is blocked by Firefox as it still uses demo.piwik.org which is on the blocking list.