Unfortunately having two unique sets of automatically generated navigation isn't currently possible. One alternative is to create your top navigation with a manual menu, your bottom navigation with a menu widget, and then disable the top-level pages from showing up in menus (found in page preferences, or by right-clicking a page in Plan mode). Since there are more pages in the bottom navigation, this could at least save some time by keeping that set automatically generated.
Is there any changes after 2 years?
I have the same sort of inquiries regarding the flexibility of separated / detached menus and submenus:
And also a few questions there, I’d love to be answered.