plugins included via network activation and templates…

Do New Blog Templates, Multisite Theme Manager, Default Theme, and Theme Switcher plugins override the plugins previously network activated on multisite?

For example, if I network activate the Infinite SEO plugin on multisite, and then create a template that EXCLUDES the Infinite SEO plugin, will the Infinite SEO plugin remain for newly created sites using the template that excluded it? (because it was previously network activated)…Or will the template override the network activated plugins during site creation and not include the previously added (or network activated) plugins, in this case…the Infinite SEO plugin?