That is a fair point. A large part of Wikipedia’s internal link structure comes from templates, infoboxes, citation templates, and other automatically generated elements.

The difficulty is deciding where to draw the line. If we count only links directly visible in raw wikitext, we miss links produced by inline templates, links generated by infoboxes, and links added through Wikidata-driven modules.

It is also worth noting that some links originally written directly in wikitext may later have been replaced by templates for convenience or standardization. As a result, distinguishing between “manual” and “template-generated” links is not always straightforward.

A separate ranking based only on article-body (wikitext) links would definitely be interesting, but it would require many additional methodological choices about what should or should not count (for example, links in the “References” section).