"...uphold the rule of law
The rule of law absolutely allows for higher level courts / institutions to step in and override the decisions/actions of lower ones. And changes to EU law are only going to make that even easier WRT critical minerals.
Local courts know this. Not that they should have any reason to be hesitant granting Talga's permits, but they IMO will be less likely to make a decision they see as being probably overturned higher up the chain anyway. They may not be able to use national strategic importance as an excuse at that level to 100% guarantee approval, but it's entirely appropriate for them to still be factoring it in to their decision.