Hi @urosk ,
For your information, the default variation selector is the dropdown interface, not the swatches. You might get these swatches from the theme or template or another external plugin on your site. In this case, it seems to come from your theme. You might want to check that again to be sure.
The Linked Variation will link different products together, but doesn’t change their product type or nature.
From what I inspected on your site, you seem to have overlapped rules for the discounts on this product.
The Bought Together deal offers 2 products to be bought together with quantity as “1x” while you have a global rule that offers 8% off the prices for the main product when purchasing it with “2x” as quantity. This disable the Bought Together rules. You can see this image for more info: https://prnt.sc/NGSte6fau4ga
So you should consider to use only 1: either the Bought Together offer or the Price by quantity. If you want to enable the Bought Together deal, please disable the Price by Quantity rules for the main product. It sets the min quantity to always 2.
Best regards.