I feel like you may have a minor misunderstanding of what this extension does - it is not a rigid system for handling chunk generation, but a flexible, general-purpose system that can you use as a base for your generator.
So, things like controlling chunk position / sizes are not restricted and up to you - e.g. you can poll dimensions from json[?"roomSettings"] before calling room_pack_load_map, or loop over your instance layers if you wanted rooms of truly arbitrary shapes.
Similarly, room selection is a matter of picking the right map to feed to loader function - the helper tool will by default export your chosen rooms into a map-of-room-maps (key being room name), so you can either export special rooms into a separate set or pick them based on name prefix/suffix.
Instances will be generated by default; there's plenty of options for filtering loaded contents.based on type/layer. Variables / creation code are also supported in a flexible way.
Keeping track of what you loaded is also supported.