It looks to me like your logic is completely backwards on this one.
Cajoling, threatening, ostracizing and assaulting people who take on non-traditional gender roles would certainly reduce the number of people who chose to outwardly express this desire. But would the absence of such coercion really increase the number of people who had those feelings in the first place?
Bruce Jenner lived the life of the uber-male, being a world-renowned athlete and spokesman. The entire time he felt that he was truly a woman. But he was too afraid to admit it in public. Or even in private. Precisely because of the social mores you are talking about.
If "The World's Greatest Athlete" can be transgender but be too afraid to admit it, the same could certainly be true for a whole bunch of skinny little kids who aren't likely to ever win a fist fight.
No, this knife cuts the other way. It is prima-facia evidence that people are being coerced into hiding their true feelings out of fear.
All that being said.... I agree that running around calling the other 95+% of people "cis" is a bit weird. I realize that we are just trying like the dickens to avoid using words like "normal" because that might hurt someone else's feelings by indirectly implying that they might not be "normal".... but really folks, it is a bit goofy. When a label applies to well north of 90% of the population, we don't usually see fit to mention it. You don't go around calling everyone who can see "sighted". Nor do you run around prefixing everyone who can walk with "ambulatory".
But we are in a transition phase, so some of this overreach is to be expected. Give it another 10 or 15 years and this goofiness should all be a distant memory. The activists will quit trying to insist that everyone use nonsensical pronouns like "Xe", and the throwbacks will quit insulting people by refusing to call them by the name they chose or by a gender other than their choice.