How are you applying the CRT effect to the pico-8 browser embed? The github looks like it's written in C, not anything compatible with the javascript pico-8 produces
I ported MattiasG's excellent CRT effect to webgl. Here's the pico-8 "plate" (HTML template) from the original conversion. https://github.com/carlc27843/pico8-crt-plate (some touchups may be needed for the latest pico8 version). On Chrome you can right click on the game embedded above and choose "View frame source" too.