What if I have multiple files that are not in the same folder? (That is the current use-case)

I think you can do weights_filenames= ['a_folder/firstfile.bin', 'b_folder/secondfile.bin']
(it will look for a common file path for both so it retains the folder structure)

Our workaround now for using a

Dataset

as we do, is to store the dataset ID as a configuration parameter, so it's always included too

Exactly, so with Input Model it's the same only kind of built in 🙂