This is the default behavior because CubeMX and CubeIDE only copy library files that are necessary for the current selections you made during configuration.
CubeMX and CubeIDE also uses HAL by default, but you can easily change it: after configuring the required peripherals you can open tab Project Manager > Advanced Settings, where you'll find the list of selected peripherals. To the right of each line you will find the used lib, by default HAL. Just click it (yes, straight to the word HAL) to be able to change it to LL, which can be done independently for almost all peripheral, so you can choose which peripherals to use either library.
Good luck!
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/Peter
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