Yes, it's clear the judge in the Arpaio case is not accepting Trump's pardon at face value. But frankly, the arguments you get in a news report are not legal arguments at all:
However, Judge Bolton is reportedly examining historical jurisprudence on the matter, including arguments that the president’s pardon powers are limited “by later-enacted amendments, starting with the Bill of Rights. For example, were a president to announce that he planned to pardon all white defendants convicted of a certain crime but not all black defendants, that would conflict with the Fourteenth Amendment’s Equal Protection Clause.”
I don't know where that quote language in the excerpt above is coming from, but it's not a legal argument, more a legal-sounding argument. However, the article references:
a 1987 ruling in which the Court said, “The ability to punish disobedience to judicial orders is regarded as essential to ensuring that the Judiciary has a means to vindicate its own authority without complete dependence on other Branches.”
Which, frankly, is at odds with the one case I've seen referenced (in this article only), Ex Parte Grossman, a habeas corpus motion to get the court to recognize a pardon from criminal contempt. There the court justified the pardon with language that, frankly, runs headlong into that quote from the 1987 case:
These cases also show that, long before our Constitution, a distinction had been recognized at common law between the effect of the King's pardon to wipe out the effect of a sentence for contempt insofar as it had been imposed to punish the contemnor for violating the dignity of the court and the King, in the public interest, and its inefficacy to halt or interfere with the remedial part of the court's order necessary to secure the rights of the injured suitor.
The entirety of the ruling that Presidents can pardon criminal contempt rests on the idea that the King could do it in pre-revolutionary times, because the courts were an extension of the King's power. I would not that, in the American system, violating the dignity of the court (contempt) does not violate the dignity of the President, and never has. The courts serve the people as a co-equal branch of government, not as an extension of the King's power to make laws (or even to enforce them). The Grossman court does recognize a difference between civil and criminal contempt:
For civil contempts, the punishment is remedial and for the benefit of the complainant, and a pardon cannot stop it. For criminal contempts, the sentence is punitive in the public interest to vindicate the authority of the court and to deter other like derelictions.
But the authority of the court under English common law extended from the King, the sovereign. The Court in 1925 saw no reason not to extend that same line of reasoning to the Presidential pardon, which means the authority of the federal and state courts extends from the President. Because the pardon power extends from the power of the sovereign to establish courts to act under the power of the sovereign; except, of course, under the U.S. Constitution, the sovereign is the people. The reasoning in Grossman, I think, skirts this point:
Nor is there any substance in the contention that there is any substantial difference in this matter between the executive power of pardon in our Government and the King's prerogative. The courts of Great Britain were called the King's Courts, as indeed they were; but, for years before our Constitution, they were as independent of the King's interference as they are today. The extent of the King's pardon was clearly circumscribed by law and the British Constitution, as the cases cited above show. The framers of our Constitution had in mind no necessity for curtailing this feature of the King's prerogative in transplanting it into the American governmental structures, save by excepting cases of impeachment, and even in that regard, as already pointed out, the common law forbade the pleading a pardon in bar to an impeachment. The suggestion that the President's power of pardon should be regarded as necessarily less than that of the King was pressed upon this Court and was agreed to by Mr. Justice McLean, one of the dissenting Judges, in Ex parte William Wells, 18 Howard, 307, 59 U. S. 321, but it did not prevail with the majority.
If there have been changes in the law since Grossman, and I think there have been, this would be part of it; that the legal reasoning of Grossman would not pass analysis today. In part because the power of the pardon does not extend to violation of state laws, and because the courts of America have never been the "President's Courts," but established under authority of the Constitution as a co-equal branch of government to the Presidency. Courts in this country have never been established as agents of the ruler's power, be that ruler Congress or the President. (I'm harkening back to my argument that the court must defend its authority in this matter.)
Does that render Grossman fatally flawed? No; but it does mean Grossman is not, as the lawyers say, dispositive of the issue. Although Grossman does reaffirm that the civil case against Arpaio cannot be pardoned, nor dismissed on the grounds of the pardon; the grounds for that extend back the the same power of the King to pardon criminal acts, but not to intervene in harms done by one person to another (civil actions). The underlying case against Arpaio, to reiterate, is a civil action. Again, I don't know if that issue has been brought before the court by Arpaio's lawyers or the DOJ; their arguments do seem carefully aimed at the criminal contempt charge, but I have to read between the lines of news reports to confirm that.
The original LawNewz article (available at the first link above) cites a trend toward "Trumplaw" by the courts, where they are opposing Trump's actions merely because he is Trump (a reference, I assume, to the Muslim bans that the Supremes keep upholding more than the lower courts do), and speculates the trial judge here wants to apply that trend to this pardon. I still contend the issue goes much deeper than that, and is a serious legal and even constitutional question. News reports are, unfortunately, the very worst way to get information about this. I'm looking forward to the court's legal opinion, when it is finally issued.