I think her point is that there is a bigger difference in gear ratios between a 50/12 vs a 50/11 (8.4%) than between a 50/11 vs a 53/11 (5.6%). SO, in other words I think you will be much happier when they install your 11/27 casette. With that being said, I do think it is unusual to build a time trial bike with a compact crank, so I hope they'll swap it out for free.

I don't time trial so I have no idea how high you need this kind of bike geared, but perhaps you should go even larger than 53. I have seen some TT bikes with even bigger front rings, say 55.

Here are some numbers to think about:

53/11 126.6
50/11 119.5
50/12 109.5
53/12 116.1
55/11 131.4
55/12 120.5

Let us know what you end up with. Its common to need to tweak a new bike a little. Cervelos seem to just wanna go fast!