Having factory tubes doesn't mean they'll pull the same bias though, its why most amps have bias adjustments (because valves vary so much). The huge stash of factory tubes won't all be matched - each set of 4 should hopefully be somewhat close in each amp but each set of 4 would have a wide variety of tolerances and pull a different bias. IMO you are not really going to hear the individual characteristic of a transformer with the MV that low (at least with differences like this), but you absolutely would hear the exact differences in tone your video is showing if the biases aren't consistent.
Like, the reason one amp is louder (and more squishy) than the other is probably 95% because its bias is hotter, 5% because the pot tolerances may be slightly different. I think as guitarists we're WAY to quick to point towards the transformers as being something that instantly has a noticeable effect on tone when 9/10 its something far more straightforward.
I'm not saying transformers don't make any difference at all, but you have to rule out other factors like valves being graded differently before assuming its that. The difference transformers would make, particularly at low MV settings where they are operating in a comfortable and linear way isn't going to be that noticeable as what the video shows.