Don't have the saddles in the mid position when measuring. Move them forward (well you only really need to do this the top B + E saddle as this will always be the furthest forward saddle with standard tuning) so that you've got about 2-3mm of thread showing.

It is pointless having them in the mid position when measuring scale length, as the saddles should only need to be moved back from the scale length in order to intonate the guitar correctly, never forwards. The more towards the rear of the bridge the saddles are, the higher up the end of the thread will sit, and I've seen some builds where the thread ends are sitting 3-4mm above the strings as a result. If this does occur to you, I'd cut off the ends of the threads so they don't stick into your palm when playing.

Unfortunately, a lot of the Tele bridge pup routs are in the wrong place by about 2-3mm, so will need enlarging. The good thing is that this work doesn't have to be particularly neat, as it will be hidden by the bridge plate. A chisel, or a sanding drum on a Dremel, are the easiest ways to do it. Just don't go wider than the existing rout as the bridge plate only just covers up the rout width, so any extra width will show.

The gap between the front of the bridge plate and the pickguard bridge cut-out is normally around 2-3mm on real Teles, though this can vary slightly on the bridge used.

So from your photo, the bridge look likes it needs to come forward by a couple of mm, which should then allow the saddles to intonate correctly. It probably means some pickup rout enlargement work, but be positive but careful and it won't take long.