if someone played on a DK with the jump button on the left. and they broke the WR would you consider that legit ?
Yes. So long as there is no in-game effect which can be demonstrated to be possible only with, for example, the button on the left versus on the right, alteration of ergonomics should have no bearing on score legitimacy. The matter, in this case, should fall under "player's choice".
This is different than, say, the Missile Command cursor settings, where the choice has a direct effect on game behavior.
There is a grey area here, however, which can be seen in games like Track & Field, where playing with a trackball offers an obvious advantage over playing with buttons, even though playing with a trackball doesn't directly modify game behavior.
It's in trying to avoid this grey area where the hard and fast 'everything original' rule has established footing, and original cabinet's staunchest defenders never seem to bend on this matter because they can always cite examples like Track & Field. The truth, of course, is that 'everything original' cabinets are virtually non-existent -- leafs have been swapped for wicos, concave buttons for convex -- and so the matter itself inherently lives in the grey area and the conversation inevitably devolves into semantics.
MAME is a separate issue. As much as you've heard the Donkey Kong discussion of keyboard versus joystick, that shouldn't ever really be a point of contention for any reasonable person. There is nothing that can be done with the keyboard that can't be done with a joystick (regarding DK), so hook a keyboard up to an original PCB for all I care. Comparisons between MAME and original hardware should revolve about how game behavior is different -- how faster processing speeds might change gameplay -- not how the user interface is different.
Sentimental arguments have no place in score adjudication, and so as much as you may believe playing with 'everything original' is the best way, you cannot with any coherent logic argue it is the proper way, at least not with any all-encompassing application.
I can think of only three universal fair-play rules: one, that input devices must have one to one mapping with inputs, except for when the game's design explicitly dictates an input device serve multiple inputs; two, that game speed must not be accelerated or slowed; and three, obviously, that the game code cannot be manipulated.
I don't see how adjusting the button configuration for Phoenix violates any of the above fair-play rules, and I will upvote.
