And I can't see why we'd need to re-invade the Falklands or deploy a full dress amphibious task force to prevent France from losing her overseas departments. Do we really want to keep those areas badly enough to fight a serious shooting war over them? Even if the answer is "yes," would it really be cost-effective to keep an amphibious assault carrier task force on standby to guard against this massively unlikely event?

Well, I´d say it depends on the scenario. If the population living there decides on independence that´s one thing. Definitely no intervention then.
If a neighboring country decides to "liberate" them against their wishes then my answer would be yes. And in that case you´d probably need amphibious ships. Because these are the ships capable of transporting and landing soldiers and their equipment. And keep them supplied without a supply base on land.

And as "to knock some oil- or metal-rich African country on its ass and take its stuff". How probable is that?

I mean, let´s be generous and assume that each of the 12 EU amphibious ships could transport 1000 soldiers and their equipment. Are 12000 soldiers enough to invade and secure an African country? After all, you not only need to secure the mines/oil wells but also the transport routes and ports.
Not to mention that a convoy of 12 such ships plus escorts probably wouldn´t stay a secret for long. Any country along its route would watch with interest.

Besides, supporting a coup would be much cheaper. Followed maybe by flying in troops to "help" restore order. (Showing my cynical side.)