@Inlinebrother yes that is the best way to do it. Set your probe offset relative to one nozzle (say the left one), then set a tool offset for the other (right nozzle). That's how I do it on my chimera. (Edit: you may then have to set the nozzle offset to zero in the slicer depending on how you set that up, else it will double account)
Also note that any tilting in your carriage as it moves around will be magnified by the offset, so minimising the offset is important when designing your print head. Difficult task with two nozzles though!
Also worth checking if the weight of your wiring causes the print head to tilt in one area. Again, with two nozzles you've got twice as much stuff in that bundle, and it will throw off the mesh compensation.
If you're still struggling, it may be worth trying manual probing (probe type P0) and comparing that against your bltouch mesh? It takes time to do, but could be a useful debug to see any differences that point to something in your setup.
Finally, I'm assuming that you've already checked you've got the probe offsets correct?