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For the 1.75 millimetre version, the heat sink is the same for Bowden and direct, so the only difference is the length of the tube. For the 2.85 millimetre version, the heat sink for the Bowden version is a little different from the direct. You still insert PTFE for 2.85 millimetre Bowden version, but it doesn’t slot in as far. For a 2.85 millimetre direct version, you don’t use PTFE at all.
I’d recommend you put the new offsets directly into your firmware. You’ll need to change the firmware anyway, so it’s a good time to account for the offsets. You can also use starting script gcode, but there’s no point doing that if you have a single Extruder.