I made a small script for parsing server logfiles and passing that data to the piwik tracking api. Basically I used this: Tracking API - Analytics Platform - Matomo (and the supplied PiwikTracker.php).
It seems to be working, because in the Visitor Log I see my page titles, urls, referers, browsers, etc. Everything that I could extract from the logfiles is there.
However, that’s the only place in piwik with real data. Everywhere else are just 0s, 0 Visitors in the All Websites view, nothing in the Locations&Providers view, also there are little country-flags in the visitor log.