Correct, Dom.
FYI (and related to your question in #1997), GES does indeed strip tags. The function cac_strip_email_anchors() in bp-custom.php (around line 37) is intended to preempt this stripping, transforming links into plaintext like this:
<a href="http://foo.com">Bar</a>
becomes
Bar [http://foo.com]
However, it looks like the filter that this function attempts to hook, bp_gfs_email_content, does not exist anywhere in the codebase :) It must have been removed at some point, maybe when we switched from our old email notification plugin to the new one. So it means that this function is doing nothing. That is to say, it's not causing the problem, but getting the function to work again would be a way of skirting whatever is causing the root problem of this ticket.
It looks like, in order to get it working again, I'm going to have to change the way the GES plugin works a little bit. So don't worry about this ticket for the time being - I'll have to futz with it :)