In this case, Apollo Team seems reluctant to support people who use "plain" AmigaOS instead of ApolloOS, and have an official support forum for "Coffin" software - http://www.apollo-core.com/knowledge.php?b=9
One can speculated that they gamble on facing legal consequences, would fit perfectly if they can bail out the entire "hobby project" and blame it on "copyright nazis".
Stop inventing controversy, Gunnar didn't even know what ApolloOS was when it first came to be. Quite a bit of people are running classicWB or regular WB3.1 setups they've brought up themselves. Apollo/Coffin came to be because there were a few members on IRC that shared their already build CF images to help out people that didn't want to or had the ability to put together their own OS image. It didn't come directly from the Apollo Team.
Personally I'd like to see a legal route to a vampire friendly OS personally, something stripped down to only the essentials with Apollo core specific drivers installed already. But as we all know this is a legal quagmire.