Running winecfg/wineprefixcreate isn't a part of the build routine, and I've never seen a build routine that said, now run our application using 'xyz'. This is the same thing. It doesn't even make sense in the first place though. If you run wine and there is no existing directory at WINEPREFIX, then wineprefixcreate is run automatically. If the user already has a directory at WINEPREFIX and they run wineprefixcreate, nothing happens. So in either one of these situations, telling the user after they've built wine to run wineprefixcreate will not make a difference.
That's not true. wineprefixcreate does more than just create ~/.wine, it also does some registry stuff (such as running regsvr32 on some dlls) and installs the 'fake' dlls.
Though it is generally a good idea to clean your registry every once in a while, and to do that I just run a script with:
rm ~/.wine/*.reg wineprefixcreate for i in ~/reg-exports/*.reg ; do regedit "$i" ; done
That deletes and recreates the registry (while leaving my drive mappings alone), then reapplies specific registry exports stored in ~/reg-exports (such as specific program settings, or registry-sensitive programs I don't want to reinstall).