Can you post some pics of the bridge itself? Is the neck properly seated in the pocket?

There is a common issue with the TL kits of the bridge route being about 3mm too far south. You can usually assemble them as is and it works fine with the kit bridge, but often there is a quite a bit more gap to the pickguard than a factory tele. Normally people just slightly enlarge the route to allow the bridge to shift a little further up the body and it's fine.

The measurement of 648mm is correct, no need to measure to the 12th and then to the bridge, just measure from the nut to the bridge - High E saddle. All of the thicker strings will need to be slightly longer so you need adjustment back from the 648mm for intonation.

You are trying to measure to the point at which the stringe leaves the saddle - so halfway up the raised bit between the adjusting screws in your pic. I can't say I've seen one this far out before, so it seems like there might be something else going on? Some more 'overall pics' might help us spot what the issue is. You could also potentially get some longer adjustment screws to give yourself a couple of extra mm if all else is looking good.