Whatever the ways are we get attuned during an LSD trip, it's quite a difference from sobriety that is true so I guess getting used to that takes some work.
I am not sure it explains all of the discomfort and anxiety though, because it happens even when you are pretty used to it and have a welcoming disposition.
I think also involved are other pharmacological effects, perhaps some direct and/or others downstream that initially produce anxiety (think adrenaline)... not all psychedelics cause this to the same extent and it is not necessarily consistent with psychedelic intensity which is another argument for something else going on.
On DOC it can take like 2 hours or more to transition and it does seem to have unusual side-effects which I don't think should all be considered typical for stim type amphetamines. On mushrooms I remember getting more lethargic, yawny and jelly-legged, but these days I get a super intense energetic feeling taking 4-sub tryptamines which doesn't go away.
I don't see what dystonia has anything to do with all this, sorry. Dystonia falls more in a range of extrapyramidal effects, very often associated as side-effect with neuroleptics. What evidence is there that the extrapyramidal system is relevant here? It is a motoric circuit whereas the origin here is not involuntary movement disorders but anxiety symptoms. Any overlap between the two is coincidental, I'm sure.
Meditation is great advice though, but it can can easily get overly intense especially when ramping up to a peak, so IMO it is better saved for a little later. On the other hand, yogic practices in general are great for channeling energies - I don't mean objective and measurable energy but perceived through experience - and I would define this broadly here to include not only martial arts type movement but also dancing. What these share is that they are options of expressing your sensations - meditation involves an open podium for them to be expressed in whatever spontaneous way and the other practices while not all free-style necessarily do stay very close to direct experience of bodily sensations.
These sensation I think are in some way caused by intensified sensation, activation of something pretty complex but still very likely involving neurological and endocrine systems which is where the adrenaline etc I mentioned earlier ties in, even if I can't be more specific.
Removing yourself from these psychosomatic experiences, for example by running away from them getting lost in thought etc or simply ignoring them can have them pent up and can add to a mounting bodyload, whereas channeling them even outside of any traditional practice can help you to at least vent the biggest parts.
I'm sure there are a lot of practices useful for this that rely on wisdom that comes from years of experience with working with these sensations rather than understanding scientifically how it works.
Yogic practices or more casual expressing though things like dancing tend to be less threatening during a come-up than meditation since meditation involves more boundlessness.
