1. The Dropbox API rate limiting system operates on the number of calls per time period, not bandwidth/throughput.
2. There may be some optimizations that could be made, but they would need to be made by the programmer of the app. It sounds like you're an end-user of Duplicacy, and not the programmer, so you may want to reach out to them regarding this. For example though, based on your description, I would suggest they investigate if they actually need to make one /2/files/get_metadata call per "chunk". For a large number of files, that could add up to a large number of calls. They may want to look into using /2/files/list_folder[/continue] instead, as that enables apps to list multiple files/folders under any particular path using fewer calls (as each call can return multiple entries).