When you add a new tree each module has its own settings for that tree quite separate from any other tree. The process of adding a NEW tree has no effect on the settings of any existing tree. This has always been the case and has not changed in any testing I have done today.
If you experienced something different you will need to provide the EXACT steps you took so I can test those.
Are you confusing “modules” with something we know by a different name? Blocks, tabs, menus, privacy???