I was actually using
https://github.com/nlohmann/json for another project I recently started and haven't published yet. That one's got my vote.
I was expecting a new command line utility for this. It never occurred to me to consider those two combined files as an archive. It actually kind of makes sense. Though it may have the downside of other people not thinking to use an archive program to extra sprite images. I think my preference is for a new standalone tool.
I think the goal of doing sprite sheet extraction goes beyond what other tools currently provide. I'd say that alone makes it worth it. Though you may have a point about priorities, and where we should best spend our limited resources of time and energy.
As for options, that seems like a reasonable start. I'd say allow a resource folder to be specified, which might default to the current folder. Allow the PRT and BMP filenames to be individually specified (relative to the resource folder), which would default to the standard filenames.
From there you can extract Layers, Frames, and Animations.
Internally, Layers are closest to the actual bitmap data, but don't generally represent an entire graphic. You need to compose several layers into a Frame to get what people would view as a complete image of a unit. You could then have a vertical strip of Frames forming an Animation sequence.
Animations sequences in particular should have metadata associated with them, describing the unit, the action, the direction, and the number of frames. I believe JSON would be good for that data.
My preference here is for JSON. XML seems more suitable for human readable content that has bits of machine readable markup. Think HTML. For computer processing of largely machine readable data, I think JSON is more suitable.