I suggest you follow this instruction step by step to get a good grip on how the reader works. I think you’re overthinking it here.
Regarding your layout: beware that EU Pallets have non-square dimensions and won’t work sideways after the chain conveyor. Also, keep in mind that you need to be within reading distance to read the RFID tags. Also, if you already have a scanner at every junction, why not make a junction each?
Hence I suggest the following alternative layout:
You could also move the output to the same side as the input at the stacker cranes and move them close together, or even make it a layered conveyor system with the input above the output as moving the horizontal axis is normally slower than the vertical one, and lifting an empy fork is faster than lifting a heavy one.
And, as a general rule of thumb, you’ll want a sensor on the end of each conveyor. If you’re feeling really fancy one at the beginning of each too.
And you should be able to get this sorting all done with a single RFID reader if you keep track of the pallets after the reader anf before they were sorted for example in multiple arrays that each get treated as FIFO stack and you move the data between the arrays.