It seems pretty much how law (specifically common law) has always worked though. If Congress thinks the law should apply to them, then Congress's job is to write a law that applies to them. The president and judicial branches are not supposed to make new laws, but rather to enforce the laws as written.

My reading of the EPA's statement here is they also wanted to mildly warn the companies that if they ever in the future want to contemplate connecting to the grid (eg. to bring down costs), they should be aware that bypassing compliance now could have expensive consequences for them later. Of course, Congress (local or federal) could also change the law in the much shorter term, so there's risk to them either way if they design without any forward thought for how to comply. On the other hand, if this inquiry to the EPA was merely requesting clarity on whether they are exempt from the reporting paperwork, but are using otherwise standard and compliant designs, then maybe the law is already working generally as intended.