So far the ways to make .mp4 are limited by final file muxer. There are just 2 muxers that available on both Windows and *NIX: mp4box (from gpac) and mp4creator. Both are stand alone programs, thus there is no way to make .mp4 as one process within either VFW or DirectShow on Windows, or whatever capture-encode-packaging on *NIX. There is a
3ivx mp4 muxer, but it doesn't support AVC.
The story with AAC audio is no better. There is no DirectShow Encoders, period! Looks like Nero Recode does it using own API, despite registering bunch of Filters with DirectShow. Regardless, all software based off Nero is CLI based and lack precise quality/bandwidth settings of faac. The only one CLI interface worth looking at is aacenc32.exe, but there is no point (even with faac outputing MPEG-2 AAC that needs to be fixed with AACPatch.exe). The only reason could be HE profile, but it is useless for now.