Appealate refers to process, not jurisdiction. An appellate court hears appeals, not original cases. There are and can be no exceptions to jurisdiction and limits on scope of the law, as per the 1st Clause. It's totally illogical to take the second clause as allowing limits and exceptions to the 1st Clause. It would destroy the balance of power intended by the creation of the 3 braches. Congress could rule over them all and do whatever it pleases.
"some in Congress have talked about applying their authority to limit the federal courts by passing a statute that would prohibit the courts from determining whether or not it is Constitutional to keep the phrase, "under God," in the Pledge of Allegiance. What's keeping Congress from using this authority..."
Is the recognition of the rest that it's an illogal train that leads to abandoning all semblence of Constitutional govm't for the creation of a tyranical Congress. One that picks and chooses which laws are open to review according to what indications come from the judiciary.
You need to talk to the Founders who used "appellate" to modify the noun, "jurisdiction."