This Addon automates the process of trying to collapse down modifiers on a mesh with shapekeys while keeping the shapekeys intact.
This does not work with all modifiers due to blender not having a reliable way of transferring shapekey information when vertex counts change in unpredictable ways (e.g. Decimate, Weld modifiers). If that is the case the addon will help you with error messages to find a problematic shapekey.
This Addon adds 3 new operators which can be found in the 3DViews Object Menu:
Select the Object you want to apply modifiers to and select one of the options.
you can also search for the operators via the Quick Search floater (Hotkey: F3) and typing "shapekey" or other keywords in the names of the operators.
Initial release as extension
This extension does not require special permissions.