Actually the problem is not in the binary definition of data but lies into data filtering/transformations and semantic/organizational changes performed by each application/libraries.
Having a common binary language would just help a little in this case. Because you will still have datas organized/interpreted differently, stripped down between a big blob collada file and an optimized file suitable for loading at runtime. Data transformation is not an easy topic, well... its even the whole purpose of a program! ;)
Things as simple as bones matrices can sometimes be interpreted/organized differently, handiness is often a concern between applications. A supposedly common format like FBX is quite a challenge to master with its handling (not-always-documented or not documented at all) of matrices/skeleton/skinning/channels/animations/handiness...etc, Add to this a bit of salt, like Maya or 3DS are exporting things differently to this format...etc