WooCommerce currently has templates for Cart and Checkout but not for My Account yet.
Yes, you can create/edit a 404 template with Cwicly.
If you use the legacy versions of the WooCommerce templates, this plugin should work fine. If you use the newer block templates, then it may not work,. This is not a Cwicly specific issue, it is based on the hooks and compatibility of the WooCommerce blocks.
If you have someone very experienced available, they can probably create compatibility between any plugin and the templates by utilising the advanced options that Cwicly provides.