Can I simply replace the AN043 *2 antenna with the AN048?

Yes you should be able to replace the AN043 antenna with any chip antenna 50 0hms. Just make sure you place a series and shunt element at the feed point for impedance mismatch transformation. The series element should be a 0 ohm resistor to start with, while the shunt element should not be mounted.

Just like in the CC2540 USB Dongle reference design?

That is correct.

If we are thinking price oriented than the cc254x keyfobe antenna design is cheaper, so actually it has the same effect. Am I right?

While antenna performance depends on a number of things from antenna type, ground plane, casing, human interaction, environment in which the antenna has to work etc. The performance of a [articular antenna depends on the size of the antenna and the cost of the antenna.

The PCB antenna is cheaper as it simply printed onto the board. The chip antenna has a cost associated with it. The performance of these antennas can be very similar with regards to range.

To answer your question, the antenna performance will be similar while the price of the chip antenna will be a lot more.