As Lydia mentioned, we obviously do not actively discourage outside contributions, and will gladly listen to suggestions on how we can do better. That being said, we are actively taking steps to make it easier for developers not already part of the community to start contributing.
For instance, we created a website about our software itself [0], which lists the MediaWiki extensions and the different libraries [1] we created. For most of our libraries, you can just clone the code and run composer install. And then you're all set. You can make changes, run the tests and submit them back. Different workflow than what you as MediaWiki developer are used to perhaps, though quite a bit simpler. Furthermore, we've been quite progressive in adopting practices and tools from the wider PHP community.
I definitely do not disagree with you that some things could, and should, be improved. Like you I'd like to see the Wikibase git repository and naming of the extensions be aligned more, since it indeed is confusing. Increased API stability, especially the JavaScript one, is something else on my wish-list, amongst a lot of other things. There are always reasons of why things are the way they are now and why they did not improve yet. So I suggest to look at specific pain points and see how things can be improved there. This will get us much further than looking at the general state, concluding people do not want third party contributions, and then protesting against that.