The question is about watchlist emails, not those sent due to some kind of subscription (did you mean Echo? or LiquidThreads?). Watchlist emails don’t support, and have never supported, HTML. But yes, you’re right that it’s connected to the email relay changes: phab:T324978#8484182.
I did not mean Echo or LiquidThreads, but I've always seen plain-text mails, including for changes in pages of the watchlist (all links where plain URLs).
Also when I was refering to user's preferences on the wiki (where there's no option allowing to select the format), this was clearly about mails notifications, almost all of them being for diffs in watched pages (and extremely rarely for mails enabled for users directly sending us a privater email via the wiki; other "subscription" options are disabled, such as newsletters or replies to talk threads).
So it's strange for me that you got problems to use messages containing links to diffs as they were always plain-text and never contained any HTML part (overriding the plain-text part when viewed). I never saw the problem you get now. I wonder if this conversion to HTML was not just performed (incorrectly) by your own mail server or provider, or by your own local mail agent, or by some local security suite installed on your system implementing some proxy, as it appears that it was never performed by the mail relay previously used by TWN
(Note: I don't use any local user agent since now many years, I just use now webmail today, hosted by Gmail, and accessible across all my devices; Gmail seems to manage plain-text mails correctly when converting them to HTML on desktop browsers or in its mobile apps; I also know that other wellknown webmail services are breaking the content of plain-text messages on their web interface. Especially Orange.fr which has lots of unsolved issues since very long in their webmail service: is it what you use are using? I've just set Orange.fr to forward all mails to Gmail instead, after just very basic antispam filtering, to keep my historic email address on Orange, so that I almost never use their broken webmail service, which also breaks on their mobile app; for lot of other reasons, I no longer use local agents, even if they implement IMAP, but I don't want any SMTP-based local agents that is deleting contents and make them inacessible across devices, and not as resistant to local OS bugs and crashes, that can destroy everything; it's also very painful and risky to make OS upgrades when using local mail agents, the local conversion takes also very long time and uses lots of local resources; alternatives using IMAP-based clients may be stable today, but too often it's very painful to manage their local filters, due to missing features in IMAP mail providers; other reasons include local security concerns). Note that this was probably the reason why TWN prefered using an external professional provider for SMTP-based services (hosting them ourself in any local LAN is very risky and tricky, STMP is a dinosaur protocol very difficult to secure, and there are too many issues, including many new ones, to follow by a single user or a small team).
In the Phabricator comment I linked above, Niklas confirmed that this was a bug with a relay used by TWN for a short time (it was not the old one, but not the current one either), not with my software. By the way, I’ve been using the same, quite mature desktop application (Thunderbird) for years now, so it seemed very unlikely that it suddenly broke (and it was not even after a major version upgrade, but months later).