GrapheneOS is currently unaffected, at least specifically regarding your freedom to install apps. They've stated this won't affect GrapheneOS.
The main problem as pointed out by floofloof is that a lot of Android development is no longer part of AOSP, but separate proprietary implementations. For example, if you install stock Android, Google has a feature to recognize music playing around you and provide a list to you later. GrapheneOS lacks this feature, because it relies on proprietary code. Same goes for the features to find your device if it's lost, AI stuff, etc.