I fail to see how any of this is intolerant, or transphobic. You might not like these opinions. Or disagree that there is good reasoning behind some of this. This does not make the one you are disagreeing with intolerant.
Yes. RMS argued for gender-neutral pronouns since more than twenty years ago. Just because it is a different set of neutral pronouns than is popular today, some people mark him transphobic. That is absurd.
Unfortunately, the more tolerant attitude of just agreeing to disagree seems to have gone out of fashion. Now the preferred option is to destroy a person's entire career and slander their reputation with deliberate misinterpretations of what they've said and done.