Okay, now I am going to sound pedantic. (noone is surprised :p)
Intonation should be done with instrument in playing position. Lying flat (as per video), will give you a slight difference to when the guitar is in playing position. Gravity is a thing. As is the drag from the pickup magnets if they are too close to the strings.
It's not a huge difference, but some players are ridiculous about intonation. I had to pay particular attention this this, because the midi guitar I slapped together was super fussy about it. If the intonation was out, even slightly, the tracking suffered.
edit : I forgot that I spent a LOT of time on the djenty bass (bead tuning) I used when we tracked the Alinea album last year. Glad I did, meant I didn't have to re-track when the engineer proclaimed both guitars to need to be setup (again) and re-track. I'll admit, I was a bit smug - a very minor win for the bassist