Per Commons licensing policy GFDL-only works are still allowed if they were licensed before 15 October 2018. Also, on local projects there are quite some GFDL-only files left that can be dual licensed per relicensing criteria. Having have to change these older GFDL works to use some different 'good template' before moving to Commons and then change back to GFDL on Commons would seem as an unnecessary inconvenience to me. It's also possible to tag new GFDL-only uploads with an additional 'bad template'. Perhaps rather we can let every project decide which way they will configure it if losing files after moving to Commons actually becomes a problem.

@Pikne The communities are free to set up the configs as they want! This ticket is to make sure the new change is reflected in the configurations where the community has not yet started taking care of the configs.
The idea is also to remove GFDL from the list of "good"-templates, but not add it to the "bad"-templates. This way they can be still moved to commons if they are marked with any other "good"-template – so one could also have a template "Suitable for commons" (several wikis have this already) that if present allows to move the file but will be automatically removed from the wikitext by the fileimporter.