MKVToolnix versions 1.0.2 and older do NOT support reading AVC at all.
MKVToolnix 1.4.0 and newer can read AVC from MP4 files and put it into Matroska. It is an official release. Storage of AVC in Matroska will not be changed.
Reading AVC / h.264 from an AVI (e.g. created with x264) will only use the "AVI compatibility mode". Playback of files muxed that way may or may not work. I will not accept bug reports for that. I do not know whether or not I will implement proper support for this.
V_MPEG4/ISO/AVC
H.264 / AVC video tracks are written to H.264 elementary streams which can be processed further with e.g. MP4Box from the GPAC package
