Yeah, but people either don't know that or don't care.
"Owoce, (w znaczeniu botanicznym) są warzywami według klasyfikacji towarów spożywczych"
"[...]So, the answer to the question is that a tomato is technically the fruit of the tomato plant, but it's used as a vegetable in cooking."
"I like vegetables except for the tomato." doesn't make much sense, tomato should be without article, unles you mean one specific tomato and in that case the sentence shoul be rather "I like these vegetables except for the tomato" to sound natural...
I've found it quite typical for Polish people to put "the" wherever they can even if it doesn't belong there (for example city names, even names of people sometimes) ;)
"the tomato" is fine here. It's the same "the" as in "The shark is an apex predator." In English this does not mean a particular shark, it means sharks as a species. In Spanish we also have this, "El tiburón es un superpredador." It does not mean a specific shark, it means the species "shark", the collective of all sharks. Here we consider the tomato as a species of plant. "The tomato is a red fruit", "El tomate es una fruta roja."