Hi Bernhard,
I have received an update from MCUXpresso team. Seems this is a bug that can be avoided in MCUXpresso IDE 11.5 that will be released early next year.
The “boards” folder appears due to the fact that IDE is trying to copy the modified files from the created Board SDK. The path to those files from the created project is identical to the ones from the created SDK: /boards/<board_name>/project_template. This is the structure of an SDK.
Due to manifest schema modification, we missed a parameter in Board SDK code. His absence cause copying files to boards folder and not to board folder.
The problem can be solved if you follow the below steps on 11.5.0 release which will be available next year:
1. Create your project and do the necessary settings with Config Tools.
2. Create a Board SDK wizard (please select the option marked with green so you can do changes in the SDK/to be editable)

3. Go to Example section from Boards tab in SDK Editor after the Board SDK was created and click on plus button.

4. A new window call “SDK Builder property editing” will open. Here you have to link the example modified before.
4a. Enter a category under which your example will be created.
4b. Click on the plus/Add button from “Example xml definition”.
4c. Choose your modified example from the new window and click on OK.
4d. Click on the added entry from “Example xml”. (If you don’t see any entry, expand/click on “>”) and click on the “Create XML...” button.
The name for the example will be automatically complete in “SDK Builder property editing”.
4e. All the errors from “SDK Builder property editing” will be resolved after the above steps and you can click on OK button.

5. Save the modification and create a new project with “Import SDK example” wizard.
! You must have the original SDK too. The modified files are copied from your SDK, but the dependencies are copied from the original SDK.


The new created project will have all your changes and will compile.
Best regards,
Felipe
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