Went through our telemetry and noticed a case where a user was connected to the server (according to Prometheus data and console output) but the plugin still limited the server to 5 TPS.
After reviewing the code it seems like the only explanation is that Universe.get().getPlayerCount() returns 0 while Universe.get().getDefaultWorld().getPlayerCount() would return 1, as this is the data source for the Prometheus plugin.
Fix: determine player count by summing up player counts across all worlds and maxing it against Universe.get().getPlayerCount().