DVD or Bluray?
Encore is not doing anything wrong; the m4a file is shorter - even if only by a fraction of a second.
While it is "legal" to put multiple files on one timeline, it is often the source of problems. This is specifically true when the audio files do not match exactly.
I do not understand m4a well, but I am not convinced that Encore will not have to process it. I did not have an option for "do not transcode" available when I put the m4a into Encore.