How to think about journal-hosted preprints, or "Just-IN" manuscripts?
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.