The <span id="..."> target is kept as is and also the <a href="#..." is not touched when sending the E-Mail.
How are you creating the E-Mail?
Are you using the Creative Designer and default templates are also via AEM as it was stated initially in this thread?
If you are using the Creative Designer, that one adds a meta tag in the header to define a base url which is then used for all relative links etc. (<meta class="nl-dce-fragment" data-nl-name="EmailUrlBase">)
That also could impact what you are experiencing on your side.
If you are not using any relative image URLs etc, you could just remove that from the <head> area and relatives URLs shall work