1.) Currently we do not enforce a size limit – what kind of data do you expect to store having size concerns?
2.) Yes you can have both kind of WebStorages! And yes use different ids to distinguish them in your code.
Changing the data from a web dashboard has no ETA yet. However, you can change your per-app WebStorage data remotely already: just change the values from your desktop and it will get synced to all your mobile versions of your game! I would, however, not use it for example for level updates (although you could theoretically), but rather for tuning balancing-settings remotely, or to test different settings how often ads are shown for example. If you add new levels, an app update is a good idea because then your app downloads usually increase and your players see there is something going on in their game and that it is making progress.