The solution is to open two instances of Wwise using the same project. Then in UE4, launch the game in editor with 2 players. The Editor will be a listen server. Make sure to not have "Use Single Process" checked. This creates two exe instances which can be individually profiled. In one wwise window, profile connect to the editor and in the other wwise window connect to the standalone version of the game. Pick any sound to solo, effectively muting the server or client.
This is very touchy though as they're both working in the same cache. Be sure to disconnect the profiler from each instance before closing any of the game sessions. That seems to have the best results on not having one instance muted until the editor is closed and opened again.