I think the problem is that the current iteration of it doesn't actually protect Leaf against a determined attacker. An earth specced jonin with a 69 earth jutsu capstone will have 23 bonus to earth jutsu from Elemental Mastery. A reasonable level for their tunneling jutsu, say... 29? Would be 52 with Elemental Mastery. They will likely have some number of buffs for earth element, but let's ignore that for this hypothetical.
If we use DoB when we make the Iron Earth Rune, the TN will be 66. That means that they will have 5 shifts of failure, so a task that would take a few seconds (making a ditch to go under the force dome) will instead take half an hour. Sure, it's not something they can do in the middle of combat, but they can certainly do so if Leaf is under siege.
While I agree with this assessment, I do think it does a good job of deterring
some types of attackers. For instance, suppose the earth jutsu in question is more HLaM than Tunnel Exacavation, and does not form a permanent tunnel that others can travel through: would they go ahead, knowing that they would reach the surface devoid of any support? If Leaf's in siege mode then I'm pretty sure Naruto + Tsunade + Orochimaru can handle any one Akatsuki essie just fine.
So the threat only materializes if multiple essies can each overpower the rune, or if one of their jutsu forms tunnels that others can use.
Then it's not good enough. Of course, though, this assumes that the Akatsuki are bold enough to try in the first place, assaulting a heavily-fortified location defended by unknown abilities of massive scale. These guys are paranoid, and who knows what else we have in store for them? Just because they
could make a tunnel into Leaf does not, I think, mean they will consider it safe to do so. (There are some other contributing factors, like how even if they can make their way in they might balk at not being able to easily exit if needbe. Broadly I just think it largely shakes out as "even if they gauge that they could, they would not feel safe doing so.")
If I were Uchiha Itachi and I was presented with this kind of defense, what I would do next depends heavily on the situation and how desperate I am. If I believe the rift is within Leaf and actively being delved, then I know that I am on a dire time limit and cannot afford to
not assault Leaf if it is at all within my means to do so. But if I believe, however, that Leaf simply needs to be destroyed for disobedience, I may feel the risk of venturing into the ultimate prepared ground not worth it, and instead blow up Tanzaku Gai and the other major Fire cities while waiting for Leaf to either come out of its shell or resign itself to eternal irrelevance. Much safer and still sees Leaf destroyed as a geopolitical entity: even if it comes out of hiding one day, the land of Fire will have long since been divvied up among all takers.
Of course, we wouldn't go into siege mode without some kind of wincon in mind, but I do think there are plausible scenarios here where the Akatsuki test Leaf's tunneling defenses and are genuinely deterred by them, choosing to stay on the outside and attack us through other means than assaulting Leaf itself.