I wonder if John picks up that Sherlock is not as much in control as he thinks he is, maybe he needs the locked room as much as John does...

I think John has a hint of it. It's why he's remembering instances of Sherlock being vulnerable, although he's unsettled by his own varying reactions to Sherlock's vulnerability. In the first instance with the cabbie, his instinct to protect Sherlock overwhelmed everything else and that inclination colours a lot of their relationship and yet in Dartmoor John reacted differently, kept abandoning Sherlock, refusing to see that he might need protection.

There are inconsistencies in John's behaviour. In many ways, he is almost as mercurial as Sherlock.