Why does adding a variant product to the cart only add the first option?

Yes, your swatches are line item properties and do not trigger variant change.

Now, the problem is due to a typo in your product-template section.

There is a code:

<p class="visually-hidden" data-product-statusaria-live="polite" role="status"></p>
<!--productAccordion-->

which should be

<p class="visually-hidden" data-product-status aria-live="polite" role="status"></p>
<!--productAccordion-->

(a space is missing before aria-live).

Adding a space back should fix it.