How to think about journal-hosted preprints, or "Just-IN" manuscripts? The NRC Research Press (or Canadian Science Publishing) offers a, at least to me, peculiar option they call "Just-IN" manuscripts. This seems to be an extreme version of an online-first article. Note: I understand an online-first article to be a basically finished version that's just waiting for some cosmetic stuff, like volume and page numbers, but gets hosted on the journal website early, and assigned a DOI. (As noted in the answer to a related question, in some journals the online-first article isn't quite the final version, but it still sounds as if it should be substantially similar to the final one.)

The "Just-IN" approach, however, means that the author's version is made available on the journal website. This happens right after it's undergone peer review and been accepted, but before it's been copy edited or been corrected by the authors. NRC notes


  Readers should note, however, that changes (sometimes substantial) are made during the publication process, so the content of the official version of record could be different from that of the Just-IN manuscript.


In other words, this seems to be something that is between a preprint and an official journal version that's just waiting for publication. Indeed, I have had my eye on a specific paper that's been sitting in this status for over half a year, and where, based on a cursory check, the contents appears to be the same as in the arXiv version (which was posted before the journal received the manuscript).

I wonder:


How different can the final published "copy of record" version be from the "just-IN" version?
To cite the "just-IN" version I would use the DOI. Given that this DOI will later point to the final version, am I potentially misleading readers if the two versions turn out to be significantly different from each other? (If I instead were to cite the arXiv version, should it exist, at least the previous versions would be available to future readers.)
How different can the final published "copy of record" version be from the "just-IN" version?


By as much as how just-accepted articles can differ from actual published articles (this is in all likelihood what the two types of articles are in this case). Copyediting is done, figures are moved, author corrections are implemented. This last part can be quite substantial, e.g. if the reviewer recommends acceptance but has a few extra (optional) comments that the authors agree with. The central arguments presented by the paper are not likely to change, but the presentation might.


  To cite the "just-IN" version I would use the DOI. Given that this DOI will later point to the final version, am I potentially misleading readers if the two versions turn out to be significantly different from each other? (If I instead were to cite the arXiv version, should it exist, at least the previous versions would be available to future readers.)


Because the central arguments presented by the paper are not likely to change, you can safely use the DOI of the just-IN version. In rare cases, this might not work, e.g. if you say something like "See Jane Doe et al [ref] figure 3" (since figure numbering might change), or if you're citing Jane Doe et al for something that isn't their central claim, e.g. "It is well known that dark matter exists [ref]" where Jane Doe et al isn't a paper about dark matter's existence, but rather its properties. But these exceptions are quite rare, and you should be able to safely cite as-is.