You're missing the point that WP Engine forked WooCommerce.
It is their version of the project and they are permitted by the terms of the license that WooCommerce agreed to make whatever changes they like.
Open source is a double edged sword. You can't leverage the benefits of the community and then deny the community the ability to benefit themselves.
> You're missing the point that WP Engine forked WooCommerce.
That point is impossible to reconcile with this phrase:
"...has been swapping out WooCommerce’s Stripe Connect Account information for its own when a user installs WooCommerce."
The verb tense "has been swapping" implies continuous repetition of the swap, not a one time fork, then "when a user installs WooCommerce" doubles down, implying it's the original code, with user install action being the time of the stealth edit.
The article's sentence is constructed incompatibly with the point you're making. Note I'm not saying your point is incorrect.