My understanding is Lyra 5.3 may have many changes to the way inputs are configured.
As of Lyra 5.2, the main reason for their organization seems to be to ensure that only contexts which are actually used on any given platform will be loaded.
For example there isn’t really a need to add MKB inputs on a console, nor is there reason to add Gamepad inputs on a PC that has no Gamepad. The Lyra 5.2 organization separates these and loads what is needed.
There shouldn’t really be much of a penalty to moving all of those into one huge IMC. If that is what your plugin requires, then you can do it. (Also, that plugin should probably be updated, this seems like an oversight to require a single monolithic IMC).