Thanks for your comment. It helped me to solve the issue.
I created clean installation of 3.0.1-b9 with clean domain, configured the domain and deployed the application. I got TLD warnings again but project is deployed with no problem - so I guess these warnings doesn't matter.
I think the problem was that the application wasn't fully undeployed - it remained somewhere in domain even if it wasn't shown in Admin GUI. Creating new domain solved this.
Now I have EE6 and MDB working.
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