Re: The Noda B’Yehuda (and some others), we see this kind of disclaimer on almost every sefer. They can’t all be meant seriously. Sefer Seder Ya’akov on maseches avodah zarah even has a disclaimer, but inside the sefer says clearly that the disclaimer is false. Have you seen the Aruch HaShulchan’s introduction to Choshen Mishpat and his unending praise to the Russian Czar? Can we take that seriously given what we know about the Russian czars? Maybe I’m being overly skeptical but I think it is clear that these types of disclaimers are a reaction to the medieval Talmud trials and the attempt to disingenuously avoid such trials and pogroms due to contemporary halachic literature. The difficulty with these disclaimers is that they appear on sefarim (such as those of the Noda BiYehudah and Chasam Sofer) in which the authors explicitly say that the Christians in their day are ovdei avodah zarah and that the various halachos in the gemara do apply to them.
Were the printers of the gemara less than fully honest when they changed words like nochri to kena’ani or kusi? If not for that we would not have had any printed gemaras for centuries. Similarly, if not for these disclaimers we would have lost centuries’ worth of chiddushei Torah. Perhaps this was an es la’asos laShem.
Yam shel Shlomo, Baba Kamma, ch. 10, no. 20, states that the Torah
is given solely to the Jewish people for their welfare. Thus, theft of non-Jewish property is not its concern, except as it affects the integrity of Jewish behavior.
Whether this concern for chillul Hashem is biblical or rabbinic is the subject of debate. Kesef Mishneh, Hil Gezeilah va’aveidah 1:2, maintains that the way Rambam codifies the law (i.e., he writes that it is prohibited, but does not say that the transgressor violates a negative commandment), indicates that Rambam is of the opinion that chillul Hashem is a rabbinic
concern.
Rema, Even HaEzer 28:1: If a Jew betroths a woman with a ring that was stolen from a non-Jew, that the betrothal is lawful, is problematic. If the ring is stolen property, then the betrothal should not be valid.
However, even those who are permissive in these areas prohibit such behavior because of Chillul Hashem.
Rabban Gamliel decreed that stealing from a non-Jew is prohibited because of chillul Hashem (Talmud Yerushalmi, Baba Kamma 4:3: “The Roman government once sent two officers to learn Torah from Rabban Gamliel and they learned from him mikra, mishneh, talmud, halachos and aggadot. When they were finished, they said to him, “All of your Torah is pleasant and praiseworthy except for these two matters in which you maintain … and in that which you maintain that it is prohibited to steal from a Jew but that it is permissible to steal from a non-Jew. At that very moment, R. Akiva decreed that stealing from a non-Jew would be prohibited because of chillul Hashem.). And Shimon ben Shetah refrained from keeping an object that was lost by a non-Jew lest he be considered a barbarian. “More than I want all of the money in the world,” he
declared, “I want to hear the Gentile say, ‘Blessed be the God of the Jews.'”
(Talmud Yerushalmi, Baba Metzia 2:5. See also Tosafos, Baba Metzia 87b, s.v. ela. Rambam’s Commentary to the Mishnah, Keilim 12:7.)
R. Moshe of Coucy, author of SMaG, put is succinctly, “All those who steal from Gentiles are guilty of Chillul Hashem for they cause the Gentiles to say ‘the Jews do not uphold the Torah (ein Torah leYisrael)’.. and they cause them to say ‘see how God chose for His portion a people of thieves and frauds.'” (SMaG, Negative Commandment no. 2, Positive Commandment no. 74. SMaG, prohibitions, no. 152; Sefer Hasidim, no. 1414. Hagahot Maimoniyos, Hil. Gezeilah va-Aveidah 1 [a].