An ecommerce form either through a Thon event or through Commerce>ecommerce does not provide the option to use custom event fields.
Within Thon you will see the option to set custom event fields but this will not display on the ecommerce check out page. Those options are showing because within Thon custom event fields are available for other forms such as registration and donation.
Placing custom event field here will not display it on the site. Going into the commerce>ecommerce>form customization. Will show that no custom event fields can be placed on a standard ecommerce form.