[CrazyWookiee]

Seems that you're stuck no matter what.

One way, you'd get a new trunk off another car. That has a risk of paint not matching and a different VIN sticker. But then for that you could get documentation so that in the future if you were to resell, you'd have that paper work.

The second way, you could ask them to patch the holes. This also doesn't seem quite as good and the paint might also not match. In that case, the new spoiler would go on, and I don't think it'd cover the holes that well, even if they patched it.

Either way, You'd probably have a risk with the paint not matching. I'd probably take the new trunk and documentation. The new trunk will have factory hardness paint, even if the color isn't 100% accurate and the documentation would protect you from future resale. For compensation you could request that they reimburse you a free spoiler for your troubles maybe?