Hi webdevandre,
Thanks for reaching to us.
I tested it locally and everything works fine https://prnt.sc/RMLtY0BErgRE.
You may confused Disabled swatches and Out of stock variations.
Disabled swatch shows that there is no product with the following combination of attributes, and they are completely not related to the status of existing combinations, neither in stock nor out of stock.
In this example, you can see that https://prnt.sc/RMLtY0BErgRE there are only blue and brown products with size M. There is no Blue/Brown variation of products with sizes L and S, so you even can’t select this combination (they are “disabled”), but blue and brown with M size can be selected because they exists and even if it is out of stock you can still select it to see its stock status.
Hope this helps.
Regards,