In the game rules, it says:

For Full-game runs, the final in-game time must be verified either by showing: The pie screen in Epilogue

My first submission shows the pie screen for 5s but was rejected for:

file time not shown during the run

Is the pie screen not enough to verify runs anymore? Or did I misunderstand what the mod was referring to?

You need to show filetime throughout the entire run AND verify the final time with the pie screen. If you want to run timerblind you can set up livesplit to show filetime if you're on PC.