Remove the settings from multiple places. Add only to TS you included via site set.

Seems like a bug: The 'Active TypoScript` ( TSOB) was showing value from Configuration/Sets/SitePackage/setup.typoscript. But the FE was using the value set in template record placed in the root page.

Details: I had a similar situation. I had to override the news template so first I added it to a TS record I had in the root page. (But the path here was wrong).

After doing a trial with site set. I added the right path in site set TS. And the object browser was showing this value. But FE was actually using the value set in the template record and not from TS defined in site set.