If I were to have my recording laid out like the image attached, and the AutoSplitter desynced (say, the game lagged for a frame or two and offset the timer from the actual IGT by a few 100ths) would that run still be valid? (given that final time is shown on pie screen)

The layout blocks the in-game timer but you have livesplit shown for the IGT and the berry counter is still visible, so this layout should be fine. Any small desync isn't anything to worry about either, livesplit is often used as a substitute for the in-game timer.