It seems that it is possible to keep the current behavior for those that want to customize the configuration of Modules/Setup.dist (knowing that they can just use Modules/Setup.local if they are only doing additions to the Setup configuration) and at the same time get rid of these warnings for those that never change Modules/Setup.dist. This could be done this way:

* 'configure' does not create anymore Modules/Setup.
* The 'Makefile' target of the Makefile uses now Modules/Setup.dist when Modules/Setup is missing.
* A developer that wants to customize Modules/Setup.dist needs to copy (only once) manually Modules/Setup.dist to Modules/Setup and to modify this last file accordingly. She/he gets then the same warnings as those that are occuring currently and in that case it is useful to have the build abort upon such warnings as proposed in the current issue.

If this proposal is acceptable then it should be implemented in another issue, I think.