Agricola - Land Parcel point
According to the rules, p8, "the [scoring] categories are scored one after another", so yes, if you consider these two categories in isolation, if you had a single unused space, you'd lose a point at the unused farmyard spaces scoring category stage, and then gain two in the bonus points category stage.

The card doesn't alter the way you score points in the unused farmyard spaces stage, it operates by providing you with (or costing you) bonus points. (For example, note that with this card, your first unused farmyard space, with only the two scoring effects operational, gets you a point, the second costs you three points, the third costs you four points, but the fourth only costs you one point.)

Don't forget that other cards might also add, or subtract, points for unused farmyard spaces and the game has to be designed so that all the pieces can interoperate with one another.
(For example, you might have a card that says something like "when calculating your score for unused farmyard spaces, you don't lose any points for such spaces"... in conjunction with the Land Parcel card, this would give you 2 points for one unused space, cost you 1 point for 2 unused spaces, and cost you 3 points for three or more unused spaces, because again the bonus points get accounted for after the unused farmyard spaces points.)