WordPress.com isn't a good comparison to WP Engine. For starters, you can't install plugins, because you're renting out a single site on a multisite network and any custom plugin code would trivially violate the paper-thin isolation between tenants. WP Engine provides separately containerized servers and databases so you can do whatever.
It's like the difference between getting an account on a Mastodon instance versus a specialized Mastodon instance hoster.
WordPress.com allows plugins on the business and e-commerce plans. Sites with plugins are hosted in isolated environments. This has been the case for years and years.
It's an okay comparison really, so long as you compare the right bits. WordPress.com has cheaper and lower-feature plans than WP Engine's lowest one ($20/month), but once you hit that same price tier ("Business" @ $25/month) you can install plugins.
WP Engine is a pure commercial WordPress hosting service, while WordPress.com also has a personal blogging service stapled on.