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.
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.
But it's extremely common to fork a project and keep it up to date with the latest commits from the original repository. Pretty much the standard in fact since most people just want to make a few small changes.
WP Engine has the legal right to make whatever change they like in their fork.
Including redirecting affiliate revenue.
MM continues to repeat the claim that WPE modified Woo itself, so WPE's lawyers are probably adding libel to the pile of claims. I think they're still waiting for a8c to file first for PR reasons.
The new to me allegation in this is this alleged WPE swap out of WooCommerce Stripe affiliate account:
WP Engine had been siphoning “tens of millions” of dollars away from Woo’s revenue share partnership with Stripe into its own coffers. It’s understood WP Engine has been swapping out WooCommerce’s Stripe Connect Account information for its own when a user installs WooCommerce.
Ripping out an OSS' revenue model would seem not great. There's a term for use of electronic communication systems to redirect money to oneself. But, not cut and dried, if the source code containing that model is fair game...
To your point, this must be a one-sided take as well, since one would have expected an accusation of 8 figure wire fraud to escalate more clearly if it were that simple.