Mastermind conundrum

My kids are now of the age where they enjoy playing Mastermind. It has been agreed that the code-setter will always use four different colours, rather than the more sneaky version where the code-setter is allowed to use two or more of the same colour.

If you use one of each colour, then logically, the 'score' (the little red and white pegs) would be the same, whether you mark the guess on the basis of the answer or vice versa, because each coloured peg only counts once, for example:

Code: Re-Gr-Bl-Ye
Guess: Pu-Pi-Re-Ye

If the code setter marks the guess on the basis of the code, the purple and pink score nothing, the red scores a little white peg and the yellow scores a little red peg.

If the code-setter marks the code on the basis of the guess, the green and blue score nothing, the red scores a little white peg and the yellow scores a little red peg.

So we get the same mark either way - a little red peg and a little white peg. So far so good.
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Question: does this reciprocity hold if the code-setter is allowed to use two or more of the same colour? For example:

Code: Re-Gr-Rl-Ye
Guess: Pu-Pi-Ye-Bl

The purple, pink and blue score nothing, leaving a yellow, which scores a little white peg.

Now, with the same code, how do you mark...

Guess: Pu-Pi-Ye-Ye?

The purple and pink score nothing, there's one yellow in the correct place, which scores a little red peg, but what about the other yellow peg? In the absence of the correct yellow peg, it would have scored a little white peg. Some sort of logic and fairness says it gets nothing, because the yellow in the code has been 'used up'.

Further, if you were to mark the code according to the guess, you'd get the same result, the yellow in the code is in the 'correct' position, so that's one little red peg and the two reds and the green score nothing.

So, that's the question: if you are playing the sneaky version where the code setter is allowed to use the same colour more than once, can you ever have a code/guess combination where marking the code would give a different result to marking the answer?