Are the AD9361 and AD9364 drop-in interchangeable (except for no RX2 in the AD9364)?
AD9361 and AD9364 are pin and software compatible.
I assume what you are trying to do is to design a board for AD9361 and have an option of dropping in an AD9364?
Your statement that the two parts are drop-in interchangeable except for no RX2 is true in general, but you need to pay attention as to how the pins are connected/terminated. This depends on your use of the part. The best way to determine how to design a board in this case is to look at Figure 2 in the datasheets for the two devices and make sure recommendations in the datasheet for pin connections/terminations are followed in both cases.
For example, pins E1 and F1 are RX2BP and RX2BN. If you use them in your AD9361 design they will most likely have a balun connected to them, but with AD9364 the pins need to be connected to VSSA. The board needs to have a provision to connect those nodes to VSSA when AD9364 is used.