The tool you are using to get info about Matroska is incorrect. MPC-HC integrates another tool called MediaInfo that is old. The latest standalone version of MediaInfo reports the Matroska output as constant frame rate.
Here is the MPC-HC Changelog: https://mpc-hc.org/changelog/
It says "Updated: MediaInfoLib to v0.7.75"
The latest version of MediaInfo is v0.7.91.