So I was following the build guide, which seems to agree with the video, when I got to the LEDs. I followed the directions in the written guide about putting the hex nuts on the top & bottom potentiometer, left and right CV jacks, and the screw into the standoff, and then put tape over the LED holes.
Unfortunately, after soldering all of the LEDs, when I went to seat the panel, it turns out that the 3mm LEDs from the BOM don't fit fully through the holes (meaning the tape for the 3mm LEDs wasn't necessary), and even worse, the panel is now permanently offset further from the board. As a result, the nuts on the pots and jacks barely have any purchase on the threads, there's now a gap between the the 7-segment display and the panel, (which came at an early stage in the build guide PDF), and the jacks are also no longer flush against the panel, which was called out in step 2.7 of the guide as being important.
I think the idea was good for the 5mm LEDs, but I won't know until I desolder and clean up all 16 of the 3mm LEDs so I can get the panel to sit at the correct height again. (EDIT: yeah, it worked out well for the 5mms at least; thankfully I could just heat+loosen the 3mms and push them back towards the board, then was able to install the panel and then heat+adjust them flush with the panel before soldering them into place again)
I'm not sure if the 3mm LEDs from the BOM on Digikey are slightly too big, or why this didn't work as planned, but I wouldn't recommend offsetting the panel while installing the 3mm LEDs (section 2.10, steps 3, 4 and 5).