Regarding this bug: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=8841
Why is mod_alias exlicitly set to run after mod_userdir? This has the effect that you can't use any Alias/ScriptAlias for ~ URLs. You would most often want to do this in order to override mod_userdir for some special settings. I can't image any time you would want mod_userdir to override mod_alias, which is what happens now. It's been like this since Ben Laurie's original hook work, but I can't figure out the justification. Joshua.
