If we are talking about the John’s Mind Bungalow Theory™, look at how soft he made Mycroft.
On the plane in TAB, John saw a side of Mycroft he hadn’t seen before. He dropped the imperious mask and showed his love for his brother. John saw all of that.
*Mycroft smokes cigarettes and watches film noir and mouths along the words*
*Mycroft being tackled by baby Sherlock at the beach and smiling*
*Mycroft looking to them for help when he is at his most scared and vulnerable*
*Mycroft getting to dress up as a fisherman and join in the fun and look genuinely happy to do legwork*
*Mycroft unable to heartlessly kill someone and then vomiting at witnessing his death*
*Mycroft showing remorse for his sister and Moriarty meeting*
*Mycroft willing to sacrifice himself so that his baby brother won’t have to shoot the man he loves*
*Mycroft being cared for by Lastrade at John’s request*
So if John has always seen Mycroft as representing Sherlock’s cold, analytical side, humanizing him means that John is mirroring how he sees Sherlock now.
And that is just the sweetest damn thing I have ever seen.