Hello,
Thank you very much for choosing our theme and for contacting us.
Custom filters are actually Woocommerce filters that have been customized a bit to be shown on any page but in any case to redirect to the shop page with the filtered product.
If the filtered products are not assigned to an attribute this attribute would not be shown in filters as it has nothing to filter. This functionality cannot be changed, unfortunately.
If you have any questions please feel free to contact us.
Best Regards