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Admin Tools simply asks Joomla to change its generator tag. It is possible for another extension to do the same. The last extension to do that “wins”, i.e. its generator appears in the resulting HTML page.

Apparently your site template's generator adds code in the templates it generates to change the Generator tag in the HTML output. Since templates are literally the last thing loaded before the HTML is generated Admin Tools cannot override it. Your template is the last extension to set the generator and “wins“.

Do note that templates ARE NOT supposed to set the Generator tag themselves, per Joomla best practices. What they are doing is as much vain as it is against Joomla best practices and common security sense (more on that below).

Please contact your site template's generator developers and tell them not to do that. It's a security risk, especially since they stupidly include the version number of the generator! If a security issue is discovered in an older version of their generated templates it will be trivial for hackers to do a search for that generator tag and attack sites.