It's usually just that the company doesn't want to have to deal with potential support calls that come in about their website not working on x os in x browser, so they do the bare minimum to disable it - then if a user complains about it not working, they can plausibly deny supporting the os/browser configuration.
This takes more effort than letting it just work. People running an OS more obscure than Linux are not the type that are going to call asking for support. We are used to supporting ourselves.
Did I mention it's the same code as a working configuration?
I think it's more likely somebody did not know how to properly parse user-agent and they blocked more than they intended to.
