those loopholes and ambiguities should be left to the courts to decide with representation from both sides of the argument making their case and not some department head full of political bias and possibly an axe to grind favoring one side.

This assumes a US Supreme Court that doesn’t exist in 2024. If you want it changed, you would have to either wait till the judges change, or expand the courts.

That’s still deferring, just to the courts instead. The demand was for Congress to not defer that responsibility, and they literally can’t do that.

Deferring to agencies was not absolute. Courts could overrule if agencies were not being reasonable in their interpretation.

Isn't the whole point of the judiciary to interpret these ambiguities though?

No, their role is a lot larger than that and plenty of legal questions don’t hinge on this kind of thing. This is specifically about whether to tend to defer to agencies on the interpretation of definitions of terms and similar things related to their mandate, so long as they remain within the bounds of reason and plausibility.

A judge could go “nope, per Chevron this EPA interpretation of ‘pollutant’ looks reasonable in this context, that complaint is dismissed, but the rest of the suit may proceed”. Now they’re expected to let those arguments play out. But answering that particular kind of question definitely is not the whole point of the judiciary.