That is a weird thing in Polish in fact. I wrote more about it in this topic. Basically, the number of exceptions (things that can be treated as animate for no reason at all) is huge.
In this example, the animate version does sound more natural to me, even if there's not much logic behind it.
the thing with animation is, that adjective has to match a noun. If you use accusative=genitive noun form, you use it for adjective too. If you use accusative=nominative, also for noun and adjective. So it could be "je cały pomidor" or "je całego pomidora". but it is not really "accepted in colloquial Polish", but more like "formal one sounds pretentious and weird".
I asked our native contributors and got this answer: "To me, the whole [of the/] tomato means she ate all of one single tomato, while all [of/] the tomato is something like a bowl containing several tomatoes that have been chopped up and mixed together and so become just tomato".