"AME should output m4v files only when the multiplexer is set to None, in which case you get separate audio and video files. Please check which preset was used and what the muxer is set to. Please let us know if it's set to anything other than None, in which case you may have found a bug".
I've now experienced this issue and, while it appears that this is the intended behavior, there are two observations to be made.
1) Import an AE project into ME. If export audio is unchecked, the muxer remains set to mp4 and the file extensions are shown as mp4 in Media Encoder; however, ME does indeed output a .m4v file.
2) Rendering same project in AE without audio however produces .mp4 file.
As a result...
"Soundless" AE files are more readily "playable" since "soundless" .m4v files are, well, virtually impossible to play. Prime example: under Win 8 desktop, click the AE .mp4 file and the Win 8 "Metro" player handles it just fine whereas the ME .m4v shows as unplayable. Unfortunately, the SAME unplayability resuls occur using Media Player, Qucktime Player and the vaunted VLC Media Player. AE really appears to do it right and it's interesting that, as of CS6, there is this encoding difference and, of course, furthur interesting that ME changed it's ways with an update at some point.
Three presets were used in Media Encoder yielding identical, i.e. .m4v files, results. H.264, Youtube HD 720p 23.976, HD 1080p 23.976 and NTSC DV 24p. P.S. renaming .m4v to .mp4 doesn't make it playable either.
AE selections were selecting H.264 from the drop down menu and leaving audio unchecked. BTW, examining the Format Options, Multiplexer tab under these selections shows mp4 as the muxer.
And, to be sure the value of AE's method is fully appreciated, please again note that AE renders generate a very friendly playable "soundless" .mp4 whereas ME's "soundless" .m4v is virtually unplayable.
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