In an ideal world, everything would be nice and level. As it stands, 0.5mm isn't a big difference and it's on the added tenon, whilst the fretboard itself seems pretty even. I've seen some fairly slanted fretboards on kits, and this is certainly not one of them. You'd normally have the treble strings lower than the bass side strings, which means the bridge sits lower on that side. The factories aren't that good at getting the neck angle just right, so if it's a bit shallow, the bridge can end up sitting right on the body, which means that you may be glad of that extra 0.5mm of height. It's not a lot, but it can make a big difference to how the guitar plays if the bridge does have to sit very low. These are kits routed from templates by fairly unskilled workers, not by CNC machines, so tolerances are 'generous'.

You could level the top of the tenon if you wanted to, to know that the bottom of the pocket is all nice and flush, there's nothing wrong with that at all. Practically, it won't make any difference as the pickup will be sitting a lot higher and the pickup wire holes are nice and low, so there shouldn't be any issues with the pickup's own output wire getting in the way of the pickup sitting properly. Though you may just want to have a look at the exit hole on the bridge rout as this can be quite high, and the three pickup cables passing through it are quite bulky and can stop the pickup sitting correctly if the hole is too high up in the pocket. I've got to work on lowering the entry to some cable holes on my EX-1 kit, and my GSM-1 also suffered from this.