This is a known limitation by the WordPress menu functions, you would need to rekey all of the menus ahead of time to be +100 or whatever you need, before Pods adds the menus to fix this. Previous versions of WordPress had a bigger problem with this, but they recently increased it in the past year or so.
Also, in the Pods setup area, you can specify per content type, whether to show the menu item in the admin menu or not. That could help resolve some of those issues, and any content types not shown in the admin menu top-level, will be added to the “Pods” top level menu as sub menu items so you can still get to them.