Kitchen Undercabinet Lighting HELP

I am in the final stages of a remodel and the tile sub told me that the MC whips sticking out of the wall just below the bottom rear lip of the cabinets will not fly as my wife wants the backsplash tiled all the way up to that lip.
So I have to rip them out and was wondering if I should just use 14-2 romex and drill a hole through that lip and bring the cable through? Also, I have MC whips already installed for upper cabinet lighting but the same scenerio does not exist so I can leave them. I may have to notch the lip top of the cabinet (rear) to get the cable close to the top of the cabinet but it is not noticeable?
How do the MC Cable wires or the romex wires tie into the transformer for low voltage lighting? Can all of this, transformer included be done either mounted under cabinet or on top of cabinet?
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Can you move the MC up a bit and put a junction/outlet box in the cabinet? Most splices are done in accessible junction boxes. Better check the fixture your planning on using, you may be heading into a detail that will look pretty bad to the discerning eye.
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