You'd still get the glass about 1mm or so too big measuring that way because you'd be including the thickness of the base of the top runner.
I use a metal ruler, and measure from the highest point INSIDE the top runner, down to the top of the lower runners, then subtract 1mm to allow a bit of space.
Best to measure at 3 or 4 points along the runners and get the glass cut to the largest possible - doesn't matter if they only go in at one end of the runners as long as they move freely.
If it's still tight you can safely shave/file a mm or so off of the top of the bottom runners - if you do it on the inside and middle dividers it'll still look ok from the outside.
Or you can wedge a length of wood between floor and ceiling about halfway down the viv to give a couple of mm space when you put the glass in.