In advance of my call with Apple Support tomorrow, and partially in light of my local Apple Store's suggestion that my ISP was at fault, I setup a new IMAP account and reviewed my iCloud and gmail mail along with my usual pop accounts.
While connected to wifi, I read and took screen snapshots of a variety of complete messages - just plain text, those with urls, embedded images and/or attachments. I then put my iPad into flight mode later in the day to see how each type of account behaved.
While there is a degree of randomness from my limited experimentation, it seems that text only messages which are on the small side, with or without urls, seem to do best across the board and are preserved offline - although one or two pop emails with very small embedded images, like an Amazon order update, are still intact a month after being received. Perhaps those have the image inline, with larger images linking to external image files.
Pop accounts whose messages have been deleted from the server via another client, and those sent from my iPad with non-trivial text, suffer the dreaded "message has not been downloaded from the server" if the original message was anything other than a small amount of plain text (or the few with small embedded images I mention above).
A previously read email on the IMAP account now showed the original small amount of text and url, but the attached file now had a 'tap to download' tag. This was also evident in the sent folder of the IMAP account in an email with an attachment generated from Safari on my iPad.
In a similar manner, non text gmail emails had embedded images replaced by icons named "profile.png" for example.
In terms of iCloud mail (which I guess Apple Store employees would not be as ready to criticise as they did my ISP), messages now showed the 'tap to download' tag for attachments, while previously read/downloaded emails with larger embedded images were now blank with the footer message "This message is only partially downloaded". I did notice a variation on this where very recently read embedded image emails were still fully readable offline, whereas those whose contents hadn't been refreshed when last connected (I.e. not reread) were still blank with the footer message. I suspect the readable ones would lose their content after some time though.
Along with the evidence of the mail app consuming unexpected background time and its overall reduced memory usage compared to pre-iOS 9, along with the time element I allude to in the last sentence above, it suggests to me that mail of any type and from any provider is subject to some sort of garbage collection/ deletion after a period of time. Or has been previously suggested, perhaps the messages have only been retained in volatile memory and not committed to local storage. If it's anything other than straight text or sometimes only small embedded (inline?) images, contents are replaced with links to embedded images and attachments, supplemented with message not/partially downloaded warnings, which will be refreshed on re-connecting for non-pop accounts. Unfortunely, where another client has deleted a message from the pop server, there's nothing to refresh and we get our headline error for our pop emails with no means of retrieving the previously downloaded content.
While minimizing storage is laudable, I personally feel that removal of the contents of previously downloaded and fully readable emails is a step too far. By all means tidy the mail app's local storage where the user explicitly requests deletion, but leave everything else untouched...
Postscript: on re-reading this, it occurred to me that the tidying up process might be discarding information it can retrieve again online, while preserving locally the data it can't. Unfortunately, that doesn't work for Pop mail that deletes the server copy after retrieval. Nor does it seem to allow later offline reading of non-trivial mail no matter what the source or protocol.