Taking off from the bottom of the nut has exactly the same effect as deepening the nut slots.
But don't do any of that until you've got the neck relief and action sorted. Get the strings sitting just above the 1st fret with a high action, and when you then lower the bridge saddles or reduce the neck relief, there's a strong chance the strings will now buzz on the 1st fret - which means a new nut.
You can set the action with a capo on the first fret, and check for playability, then adjust the nut height. It's a lot easier to cut the nut slots than keep removing the nut and filing the bottom.







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