What I currently know about .mgm game files

Known info about .mgm file format

The .mgm file format is used by the three Madoka Magica TPS games released from December 2011 to October 2012. The format is likely part of a proprietary game engine used by the game's developers, Mebius Co. Ltd./D-Mebius. 
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The first 12 bytes are mostly made up of 00's, but there are three places in the first 13 bytes where they aren't 00's.
The first, fifth, and ninth bytes don't use 00, but instead use a seemingly random hex digit. I don't know what the purpose of this is at the moment.

Examples
stage0.mgm from Puella Magi Madoka Magica TPS FEATURING Mami Tomoe (jp.co.fwinc.madomagimamiTPS)
0C 00 00 00 05 00 00 00 05 00 00 00

stage1.mgm from Puella Magi Madoka Magica TPS FEATURING Mami Tomoe (jp.co.fwinc.madomagimamiTPS)
0C 00 00 00 08 00 00 00 04 00 00 00

stage0.mgm from Puella Magi Madoka Magica TPS FEATURING Homura Akemi (jp.co.fwinc.madomagihomuraTPS)
0C 00 00 00 09 00 00 00 04 00 00 00


After the first 12 bytes, the .mgm files all declare which skybox is to be used in the level.

Example
73 6B 79 30 -> sky0
sky0 corresponds to an image in /res/drawable-nodpi/ called "sky0.png".


After the skybox, a 16 byte space is added. The 13th byte uses a seemingly random byte.
00 00 00 00 00 00 00 00 00 00 00 00 0X 00 00 00

Example
00 00 00 00 00 00 00 00 00 00 00 00 07 00 00 00


After the space, textures to be used in the level are declared. Depending on the level, skybox elements are also declared afterwards.
Examples

69 6D 61 67 65 34 -> image4
73 6B 79 31 -> sky1

69 6D 61 67 65 34 00 00 00 00 00 00 00 00 00 00 00 00 04 00 00 00 73 6B 79 31
image4................sky1


After declaring the skybox and textures, the level data itself is presumably the data that takes up most of the file.

The file ends with 12 bytes of 00 hex digits.
00 00 00 00 00 00 00 00 00 00 00 00