Yes, ISBoxer allows you to launch multiple D4 and other Diablo series games on one PC, using Battle.net.

Quick run-down of setup, beyond the "install" step...

1. Use the latest Development build of Inner Space. This provides the latest fixes that are not yet pushed to the "Live" build. (Right click IS, select Patcher, click Development tab, click Install Now to actually install it.)
2. Use the ISBoxer Quick Setup Wizard. Not really that difficult, mostly just pick Diablo 4 and click Next some times. On the Characters page, select the Diablo IV - Launcher profile, because as you've discovered, launching the client directly was disabled at release.
3. After completing the wizard, Export to Inner Space
4. Launch your team



The game launching process while using Battle.net looks something like this:

1. close the launcher (Battle.net) if it's running
2. start your team
3. first launcher comes up, launched by ISBoxer. if the launcher was already up NOT from ISBoxer, then the launcher is NOT opened through IS
4. log into the first launcher (only required the first time you do this) and click Play.
5. the first launcher should close automatically when the first window comes up and is recognized by ISBoxer. if it does not, close it so ISBoxer can launch the next instance. if the next launcher does not come up for you, select your character set again to continue the launch process. (In other words, just keep repeating these same steps until all windows are open)

Each "Character" in ISBoxer (which for Diablo games I typically just call "one" and "two" and "three" and "four", to indicate which *account* I'm on) will store its own login information after logging in the first time.