Has to do with the Warp mechanics. Each border has a trace amount of tachyon radiation, which causes a warp field flux, and inverses the quantum infusers. When that happens, you will end up several light years off of your actual heading when you cross said borders.
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Trust me, it's totally Canon
subspace fields are actually forcing the players to move along a specific route which will throw them off their intended course.
I know what you mean, and most of the time you end up facing backwards, especially when crossing sectors up and down.
I also noticed that the auto navigate takes you to the centre of the arrow rather than the closest corner edge of the sector.
It's like the old saying "they can put a man on the moon, but they can't even fix the quantum infusers to prevent warp field tachyon drift"
I love your signature. TNG 'Brothers' is a gem.