Color change in theme settings not applied to custom template

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Hi everybody,

For some products i use a custom template.
When i change the color of the links and buttons in the product pages theme settings, the changes are not applied to the products with the custom template.
So, when i make the "add to cart button" green, the button is green everywhere, except for the products with a custom template.
Is this expected behavior?
Does anybody have any idea how to solve this?

Thank you,