Now, if there are simply two features, that if used together, fail for whatever reason? That's clearly a user pitfall, and should be fixed. But to endlessly try to support the Nth scenario is unsustainable.
Edit: Also, taking a look at what the author was(here: https://github.com/discourse/discourse/blob/master/docs/INST...), no wonder they want to use a system like Docker- it's an incredibly complex, full-featured setup. This isn't one-purpose software, this is a monolithic solution, that if you want to modify, you've gotta dedicate real time and effort toward.
This means that if you don't want to use defaults, you'll be constantly getting further and further away from the master project, which makes updating and maintenance so much more difficult. In which case- aren't you already signing up for the long haul, here?