Hi,
First of all, before attempting to answer, I just want to say that I totally "get" what you are trying to accomplish (I read your thread about "Natural Sound") and in a sense I am trying to accomplish the same thing! In an ideal world, we would have speakers that offer very low level resolution, are highly dynamic, and with a perfectly flat frequency response. But that does not exist (not that I am aware of), so we have to make choices.
I love this video (possibly also because it reminds me of time spend in Japan) - a bunch of audiophiles in awe over a 1950s single driver speaker:
Apparent contradiction ? No.
But to get back to the subject matter...
There is no doubt that system recordings are never going to fully capture the in-room experience. So even if the author of a video claims that the sound is representative of what he/she experiences live (meaning, in the room), that cannot be the case. He/she is probably refering to one aspect of the sound, just as we may be focusing on one aspect when we watch the playback. Recordings, especially with the microphones used here (iPhone build-in mic, MV88+, my Superlux 502s...) do not have the resolution of our ears. Microphones, ADCs, introduce distortions (frequency response, dynamics..). Also, the way a microphone captures the sound is not how our ears and brain "hears" it.
Once that recording is made, whether you listen to it on headphones, or on speakers, this is not going to change any of the above. You cannot recreate what has been lost.
What will change is whether you are adding the reverb of the room or not, and the extent to which you are introducing more distortions (other than the rooms'). This has been covered before, and I don't think we need to go over it again.
So we are limited in what can be assessed from a video, and I doubt that in the video I included above, we can get a real feel of what it was like to be in that room. As a result, we can only use videos to evaluate some aspects. Whether people who watch and use these videos are aware of this, I don't know.
So to answer your question, provided the digital version is of reasonable quality, I don't think it is much of an issue to use it to compare with a vinyl playback in the original room, because the recording of the system itself is never really going to capture the in-room experience anyway, and those subtle differences between sources will probably be lost anyway. I know some people will disagree with this - I am exaggerating thins a little bit to get my point across, you can always find some examples to contradict all this, and it remains a point of view.