Interleaving mono files to make a multichannel file is a very common operation in CDP, and is supported by "submix interleave"
and "interlx". Similarly, splitting a multichannel file into N mono files is done using either "housekeep chans" or "channelx". On the PC, Soundshaper automates these steps in many cases, and possibly Soundloom too (or a patch can be written to do so).
Many of the processes in CDP are inherently mono - e.g. in the distort programs, it is unlikely that zero crossings will coincide across multiple channels. the error message "Application doesn't work..." almost always applies to such situations - except where indeed the wrong type of file is presented!