BP is being added on top of an existing system with its own HTML emails and unsubscribe text and link. This is done by adding a filter to wp_mail which sets the content-type to HTML and adds an unsubscribe link. We have our own custom HTML versions of welcome, reset password, email verification, account activation emails and some more. bp_email_use_wp_mail has been set to true so it sends via our wp_mail implementation.
The problem is that the BP emails are not being sent as HTML and it seems that the plaintext email templates strip out all HTML tags.
Is the option here to override the existing BP emails with our own versions or can we make BP use its HTML templates with wp_mail?
BP provides unsubscribe functionality, so you maybe don’t need to do that anymore. BP Email sends html emails when possible.
You might try filtering your messages in other ways. Have you read the “customizing emails” how-to? it includes an example of overriding the BP template so that the BP content is sent in your custom template.