The point of "embrace, extend, extinguish" is primarily to get rid of any potential future competition. So, for example, it would not work if Facebook tried to do it with Twitter since the latter already reached critical mass and can stand on its own without outside help, barring bad leadership. It typically only works if the party that's being "embraced" is smaller than the company that's "embracing".

To your point of ActivityPub being open source: that's true, so Meta is, legally speaking, free to use it. However, barring any restrictions in the license, they're also free to add any proprietary features to Threads that don't work on Mastodon. It's similar to Google Chrome: Google has their open-source Chromium web browser, but they also have a version called Chrome that has features that are not open-source.