Sounds like it should work, and if you think you might change the structure of your save files in the future and would rather just have to change the normal save files (for a desktop/console export) and not worry about also changing how PlayerPrefs saves the data then that approach might be less work in the long run. Just be sure to either ensure backward compatibility, or change the idbfs subdirectory if you do make any changes that break backward compatibility and you actually want to lose the old data.
On the other hand, if you don't think you'll need to mess with the code for save file structures, it might be easier to just pop in the class to override PlayerPrefs for HTML5 exports and be done with it.