I've done a quick test, and remuxed a fansub mp4 into mkv:
[Arienai_-_Conclave]_Ginban_Kaleidoscope_-_07_[H264_-_AAC][4E67292C].mp4 144,508,229 bytes
[Arienai_-_Conclave]_Ginban_Kaleidoscope_-_07_[H264_-_AAC][4E67292C].mkv 144,472,592 bytes
Matroska is smaller in this case, but only 35 kB so... which is pretty irrelevant, if you ask me. I'd use those 35 kB with chapter information, though (even though I don't think it needs that much).