While I could answer all the issues raised by the OP, I won’t. Not only that I will concede that there is some merit and truth behind what is being said there. I’ll even take it a step a further and acknowledge that there is truth and merit in some of the other criticism of the Yeshiva World not mentioned in the OP.
In fact whatever group you are part of you should realize that there is probably some truth behind the criticism other groups have of yours that you shouldn’t just ignore or assume they are wrong because you and your leaders know better.
Now back to Chabad. As a secular historian discussing the frum world of the 20th century put it. Chabad in the 1950s was unique among the frum groups that they were the only group who was only answerable to their rebbe and was willing to ignore the VEHEMENT opposition of other frum groups. This in turn led to serious problems among the movement which by the end of the century had raised their rebbe almost to the point of deification (R’L) L’havidil Rav Hutner in the 1950s also predicted where Chabad was heading because of the above assessment. I mention a secular historian only because he would be thought of as more neutral.
There is what to complain about Chabad even without the messianic and borderline deification of the rebbe. But admittedly when it comes to that you can brush it off by saying that other groups also have what to criticize, complain and say they are doing the wrong thing about. Those things however don’t push anyone behind the pale of Orthodox Judaism. The messianism and borderline deification of the rebbe R’L do. It’s absolutely unacceptable. It’s not a question of relying on non mainstream shittos in halacha or questionable haskafa . It’s a question of the Ikerey Emunah and Avodah Zora R’L. You just can’t ignore the vehement opposition of so much of Klal Yisroel when it comes to a thing like that.