Calibre will update the title metadata field for a copy of mobi file (if needed it will first convert epub or whatever format is available just like it would if you used "Send to Device" instead of "Email to") and email that copy. That copy file's metadata for title field will containing the series info and Kindle will just display it as it would do for any other book... no tricks.
Not sure what you're referring when you write about reader <> Calibre matching books?
Are you referring to check-mark icons that are displayed in "On Device" and "In Library" columns when you're switching between "Library" and "Device" views (when you have you have your Kindle connected to your computer and Calibre detects it)?
No idea how that matching of books works: is it using title + author combo, is it using Calibre's book ID, is it using ASIN values [Calibre fills in ASIN with the same value it uses for book UUID])? I would have to do some testing to answer that question / make a guess ...
Because I'm only using USB sideloaded azw3 books... not using "Cloud"/"Personal Docs Archive" / "Send to Kindle" at all.
All I can tell you right now that in that use case (USB sideload from Calibre; that also triggers metadata plugboard that changes the title metadata to add series information) the matching for In Library / On Device books works even though the title metadata differs between the library copy (no mangled titles, so no series info) and on-Kindle copy (where title contains series info). And I'm also storing that "is it on my Kindle" information in custom column in order to have access to that info without needing to connect my Kindle first... so I can do all sorts of filtering ("show me only standalone books that are not already on my Kindle?") of my library.
The difference that first comes to my mind (and that could hypothetically be the reason for that matching not working) is that once the book goes through Amazon's Personal Docs service it will change book's ASIN Id value... it will no longer be the same as the value for the copy of that book you have in your Calibre library.
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