You cannot have two distinct paths for Auto Defined SoundBanks and User Defined SoundBanks. They will stay in the same hierarchy. However, the Generated SoundBanks folder itself, as well as every single platform, can be located wherever you want on your storage device.
It's definitely recommended you create your own hierarchy that suits your needs. For example, considering a very big project using Perforce and a Workspace with exclusions, and a lot of custom platform files (audio and not), you might have the following hierarchy:
/Project
/Project/Audio/Wwise
/Project/Audio/Wwise/Project.wproj
/Project/UE
/Project/UE/Contents
/Project/UE/Audio (your new Generated SoundBanks root path - mandatory - you need the ProjectInfo.json file in it. Path in your Wwise project is ../../UE/Audio)
/Project/Platforms
/Project/Platforms/Android
/Project/Platforms/Android/Audio (path for this platform would be generated at ../../Platforms/Android/Audio in your Wwise project)
/Project/Platforms/Mac
/Project/Platforms/Mac/Audio (path for this platform would be generated at ../../Platforms/Mac/Audio in your Wwise project)
/Project/Platforms/Windows
/Project/Platforms/Windows/Audio (path for this platform would be generated at ../../Platforms/Windows/Audio in your Wwise project)
Using such structure allows every developer to retrieve the Mandatory "Generated" platform for your Unreal by default, and blank out all the optional platforms unless you actually need them. The root for the Generated SoundBanks folder is written in the UE project, but it can be anywhere too, as long as the ProjectInfo.json file is located.
Might not be recommended, you need to explore according to your own needs, and such solution is harder to maintain and figure out at a glance than a basic one... but it's now a possibility.