Well, after submitting my changes to Tiled, and discussing it with the maintainer, we decided that instead of working around their goofy hard-coded ommision of the collision layer, it might be worthwhile to completely rework the command-line flags for including or omitting layers. So instead of working on Robo-Ninja directly, I spent the evening working on Tiled.
Specifically, adding command-line flags to their export utility that let you specify layers by name to omit, and let you also tell it to just use the visibility settings of the map itself.
This code is all in C++. I haven't written anything in C++ in YEARS.