I'm afraid you'd have to raise that feature request with Dropbox, not Akeeba. We can only use the public API they publish. The public Dropbox API, as it stands, allows you to link the entire Dropbox account to an application.
The other alternative offered is an application directory, over the location of which you have no say. However, this solution has two problems.
First, as I said, you don't have a choice over where this folder is located which defeats the purpose you want it for: all backups would end up in the same folder for everyone.
Second, it's an either/or proposition, meaning that we can either offer access limited to the one fixed directory OR let you define the directory you want to use. We cannot give you a choice between the two.
As a result it didn't make sense using the app-specific folder approach. It'd be more limiting and wouldn't offer any advantage to our clients.
I doubt that Dropbox would ever offer the feature you are interested in. From their business perspective one Dropbox folder = one individual (person). The solution they would prefer you to follow is to create a different Dropbox account for each one of your clients. Then you can share the backup folder for that client with your account so that you have centralized control over the backups and your clients are isolated from one another.
However, as I already said, this is something you have to take to Dropbox. We can't offer access control on your Dropbox account that Dropbox itself doesn't offer because, well, we're not Dropbox Inc :(
Nicholas K. Dionysopoulos
Lead Developer and Director