Everything you say is completely correct. But useful? Or worthwhile? Or even efficient?
The goal is not to find out why some users are disoriented and some are not. Well, I guess indirectly it is. But getting there with rigor is a nightmare and to my mind not worthwhile in most cases. The hypothesis developed from the usability test would be “some users are disoriented during checkout”. That to me would be enough evidence to actually tackle that problem of disorientation, especially since to me 3/5 would indicate a relatively strong signal (not in terms of telling me the percentage of users affected by this problem, just that it’s likely the problem affects more than just a couple people).
The more mysterious question to me would actually be whether that disorientation also leads to people not ordering. Which is a plausible assumption – but not trivially answerable for sure. (Usability testing can provide some hints toward answering that question – but task based usability testing is always a bit artificial in its setup.)
Operationalizing “user is disoriented” is a nightmare and not something I would recommend at all (at least not as the first step) if you are reasonably sure that disorientation is a problem (because some users mention it during usability testing) and you can offer plausible solutions (a new design based on best practices and what users told you they think makes them feel disoriented).
Operationalizing something like disorientation is much more fraught with danger (and just operationalizing it in the completely wrong way without even knowing) than identifying a problem and based on reasonableness arguments implementing a potential solution and seeing whether the desired metric improves.
I agree that it would be an awesome research project to actually operationalize disorientation. But worthwhile when supporting actual product teams? Doubtful …