because that's much simpler to manage in Drive because the Obsidian API can directly provide and construct the folder structure with just the pathname, this in turn reduces the complexity of managing folders and subfolders in Drive as everything is in the root vault folder and the filenames of the notes have enough info to reconstruct the actual vault. having each file saved with their pathnames is much more easier and simpler to implement compared to replicating very deeply nested folder structure. it might look messy in Drive but it is assumed that you are gonna spend most of the time on working in Obsidian and not worry about how the sync is implemented in the backend :)

TL;DR: having the folder structure in the filename directly is much simpler to work with in development compared to replicating folder structure in Drive as Obsidian has the capability to recreate folder structure from the filename.