No, you're the one that doesn't get it.
Either you're in compliance with the law or you aren't. I'm sure those companies are capable of determining which is the case, and making decisions based on where they want to be.
The government should not be picking and choosing which laws to enforce -- if the law is bad, get rid of the law. If the law is good, enforce it. Pretty simple.
And the government should damn sure not be in the business of using its money (that is to say, taxpayer's money, no money rightly belongs to the government) to pay fines on behalf of companies that didn't follow the law because the government told them they didn't have to. That's just insane. Hell, at least waive the penalties if you're going to do that so there's no taxpayer money lost. But then it makes obvious that you're treating companies that do business with the federal government differently from other companies, which no doubt is why they aren't doing it that way.
This is banana republic stuff.