I don't know quite what's going wrong in your case, but I call tell that when mercurial says 'unrelated' it means: the two repositories do not have a root or roots.
Normally a mercurial repository has a single root, revision 0, and any repository with that same root can push to it. A repository can have multiple roots, usually the result of someone doing a push -f.
So what you're doing in Scenario one, should exactly work. If it's not then either your apache configuration is pointing http://SERVER/HG/B somewhere other than you think it should be (perhaps a bad RewriteRule or RedirectMatch or ScriptAlias, or your Repo B didn't clone from Repo A like you thought it did, or Repo A or B changed fundamentally after B was initially cloned.
There are some tools that will alter the hashcode of your root (revision 0) node if used to modify that node: mq, histedit, strip, rebase, etc. And it's because changing the hash completely alters the repo that those tools are disabled by default and for use on local, un-pushed changes only.
To start debugging this, go onto the SERVER and see what happens if you do do incoming or outgoing between repos A and B at the file system level. If those complain then you know it's not apache, and if they do, then it's something your Apache setup.