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?