I understand what you are saying and where you are going, but your premise is flawed. Just because it's hard to comply with a law doesn't mean that the law doesn't restrict what it says it restricts. Just because enforcement for a particular crime is rare or even almost non-existent doesn't mean that there's no law against it or that the law must be interpreted differently due to the level of enforcement.
For years, in TX (before the initial CHL bill passed), if you bought a handgun, per state law there was no clear way to get it home legally. There were some exceptions in the law for things like traveling and going to sporting events that involved that particular type of handgun, but the way the law was written, you were technically breaking the law as soon as you left the store's property and were still in violation until you got home. The handgun had to be locked up and unloaded or you were in violation. And no, there were no FFLs denied in TX because it was very tricky to get a handgun home from the store without breaking the law.
The issue then and in this case is enforcement. The cops weren't standing around outside TX stores that sold firearms waiting to arrest people who bought handguns--they COULD have but they didn't. The feds aren't staking out school zones trying to catch people violating the GFSZA. They COULD but they don't. But in BOTH cases, if something goes sideways, the presence of a firearm could be an issue. People did occasionally get in trouble for possessing handguns in TX back in those days. And as we see in this case the feds will prosecute GFSZ firearm possession cases in some circumstances. Simply knowing that fact is probably enough to keep most people out of trouble.
If Metcalf had known the law, he almost certainly wouldn't be in the pickle he is. Similarly, a person who transports firearms through GFSZs and knows the laws can take precautions to comply with the law, or, at the very least, can be careful not to self-incriminate. For example, if a person were buying a firearm from a gun store in a GFSZ and didn't have a qualifying license that covers the gun in question, it wouldn't be smart to take a selfie standing on the public sidewalk outside the store with the gun and post in on social media.