When you add an extension to in_dshow config, Winamp will then use whatever DirectShow filters are installed on the system to decode the video/audio content. In other words, it won't use any other input plugin such as rarewares/audiocoding in_mp4, so installing that plugin will have no effect whatsoever (apart from stealing mp4 association from in_dshow).
Maybe try the suggestions from here
Nero Digital Information Thread
In order to use other DirectShow based player with Nero Digital streams including chapters,subtitles and multiple audio streams, install the latest ffdshow (and enable h.264 and aac decoding in ffdshow) and Haali Media Splitter (MatroskaSplitter). For a proper subtitle support with ffdshow (ffdshow subs a bit buggy), install the latest VSFilters.
(you can find all the relevant links there... sorry, I was too lazy to edit them in)
Apart from all that, sorry, but I don't have Nero Recode or any sample videos, so I really aren't sure, heh.
When one of those mp4 videos are playing, what audio filter does Winamp say it's using (c/o right click entry > View File Info)?