... is there an external program that i can use with MC to encode to AAC?
MC has had the external encoder option for years. It isn't anyhow related to a specific program or format because it simply forwards the user defined command line string, but it is possible to use it with external AAC encoders. A forum search should find more info.
In general, I wonder if JRiver could re-investigate the possibility to add a plain MP4 container tagger that would only allow to edit and add metadata. It would have nothing to do with a specific encoding format that is used inside the MP4 container files (which can contain audio and video streams in various formats).
Historically the tagger components have been integrated in the decoder plug-ins, but it shouldn't be very difficult to create a tagger that would work work with externally decoded container formats, like DirectShow decoded MP4 (also the ".m4a" files are in the MP4 format).