The general sens of “et encore” in a sentence is to mark opposition in an “ironic way” to the general idea of the text. In your example:

Il a dû payer 200 euros de réparations de voiture, et encore, il a eu une remise.

The general idea is high cost of repairs (200 euros), but “et encore” marks opposition to this idea (remise=discount). So if I’m asked to translate your example I say:

He had to pay 200 euros to repair his car, in spite of the discount

To my knowledge, “in spite of” marks here the opposition in question.

Your second example describes the same principle of “et encore” use.