LTT has a video where they tried to see how many PCIe riser cables they could string together before it stopped working.[1] They got to several meters. Maybe you could argue that it's worse inside a PC case since there's more EMI, but it seems like your PCIe riser cable would have to be very out of spec before you'd notice anything.
It might have to do with the USB buffer on the Ender. If the buffer is too small (e.g. 4 gcode commands or so) then when the buffer is filled with commands that execute very quickly, its possible for the printer to empty the buffer before new commands come down the pipeline from Octoprint. This causes the printer to stop the printhead sharply, which can cause quality issues on prints, or maybe even print failure if the sudden stop causes the print to detach from the bed.
[You can fix this if you're using Marlin](https://www.reddit.com/r/ender3/comments/btjk22/octoprint_is...), since Marlin allows you to configure the buffer size. Generally more buffer is better, but do be aware that increasing the buffer size will cause the printer to be less responsive to the "stop print" command on octoprint (since the printer will continue executing the commands that have been buffered).
[1] https://www.youtube.com/watch?v=q5xvwPa3r7M