When linking main tags in Meta with [tag:any-tag] in a comment or post, they are rendered as main tags into the full link:
<a href="https://stackoverflow.com/questions/tagged/any-tag">any-tag</a>When using tags in the user's profile, they are being rendered as a relative link:
<a href="/questions/tagged/any-tag">any-tag</a>Which makes them become Meta tags on the user's Meta profile, instead of remaining a main tag like anywhere else on Meta (for this we have meta-tag).
For example, clicking on any of the tags on Martijn Pieters's Meta profile will get you to an inexistent Meta tag, while switching to his Main profile will reveal the real Main tags.
Discovered following this Meta question.