I'll answer your questions from a British perspective, as I'm not sure how an American English speaker would use the word:
1. Definitely not. A 'villa' is large, elegant and spacious, probably two or three storeys. I think that the first dictionary definition is misleading. 'Villa' is actually an Italian word for a large detached house. The English usage dates back a hundred years or more, when wealthy British people would spend the whole summer in a rented house in Italy or elsewhere in southern Europe, in the country or by the sea. A 'villa' is large by today's standards, but would probably have been smaller than the enormous houses that some wealthy or aristocratic British people would have lived in in the past.
2. You might call them villas, especially if they are large and surrounded by their own garden.
3. Again, I'll give you the British definition, because the American usage of these words is very different. If a British person asks you 'Do you live in a house or a flat?' , they want to know if your home takes up the whole building or just part of it. If you have neighbours above or below you in the building, this would be seen as a 'flat' ie part of a building. If your home occupies the whole building, even if it is small, you would call this a house. Most houses in Britain have two or three storeys, although some only have one (these are called bungalows - but they're still 'houses') . Many old houses that have three, four or five storeys - and are too big or expensive for one family to live in - would be divided into separate 'flats'. So if your home was just one floor of this house, you would say that you lived in a 'flat'.
The word 'apartment' is an American word which is more or less the equivalent of the British 'flat'. We sometimes use the word 'apartment' to refer to a furnished apartment which you'd rent for a holiday (vacation), or a furnished set of rooms in a hotel.