You have just completely over-complicated your entire app architecture. You get around the scoped region navigation issue by creating a simple IRegionManagerAware custom region behavior. This solves just about all of your problems with navigating within scoped regions. It also allows any View or VM to get access to the proper RegionManager by implementing a simple interface.
Right now, you are using a work around that will just cause you to have make more workarounds for things that are normally supported, just like your "Global" EventAgregator, because you broke the ability to use the EventAggregator by having two bootstrappers. Everything that gets created in the bootstrapper has now been duplicated as separate instances, and when you click the button to show another shell, you have three, click it again and you have four, and so on. This include modules being unnecessarily loaded multiple times, type registrations, RegionAdapter mappings, etc. I am pretty sure all of that is staying in memory as the singleton objects have been rooted in your app. There are a number of other possible issues you may run into that isn't obvious at the moment.
By all means, use two bootstrappers if you like. Maybe your app is simple enough to where you won't run into many problems. But, I personally would never advise any of my clients to take that approach.
Right now, you are using a work around that will just cause you to have make more workarounds for things that are normally supported, just like your "Global" EventAgregator, because you broke the ability to use the EventAggregator by having two bootstrappers. Everything that gets created in the bootstrapper has now been duplicated as separate instances, and when you click the button to show another shell, you have three, click it again and you have four, and so on. This include modules being unnecessarily loaded multiple times, type registrations, RegionAdapter mappings, etc. I am pretty sure all of that is staying in memory as the singleton objects have been rooted in your app. There are a number of other possible issues you may run into that isn't obvious at the moment.
By all means, use two bootstrappers if you like. Maybe your app is simple enough to where you won't run into many problems. But, I personally would never advise any of my clients to take that approach.