@Qville I have tried with the Pen theme, tried to activate and deactivate WPFTS Pro on my dev machine, but unfortunately I can not repeat the issue that you faced with. The posts on the main page are always ordered by "Publication Date (descending order)" does not matter whether WPFTS active or not.
Could you please try once more to activate WPFTS and deactivate it on your website and see if there any differences? Could you make a screenshot or give me a link to your website?