I'm sorry, but if you modify the file manually like you did, the peripherals tool will not work properly and the validation of conflicts would not be handled properly.
Here is the documentation section that I mentioned:

Yes, we are aware of the differences from the Pins tool. The pins tool is the only tool that supports having multiple functional groups in default init. The peripherals tool has one additional level of individual components that you can freely enable and disable them in components view. You can also control initialization order of those individual component functions within the functional group.
For example also in the clocks tool, you need to have one default init configuration and the others are alternatives.
If you'd like to have the initialization split in multiple functions or controlled by some login in your code, you can omit calling default initialization completely and just call the functions that you need in your application module directly.
Wth this approach, you might also want to un-set the [B] icon (boot init) checking in the Problems view:

If the [B] icon is unset, the cross-dependencies from other tools will be checked to be fulfilled by any functional groups, not just by "default init" one.