Hi Julian,
The writer's of the document you have referred is in the process of making a change where the Rzero resistor is removed and the measurements retaken. The biggest reason is for the issues to which you are describing. The Rzero resistor can drift, which will add error to your system. Also, if the current is a little different from one IDAC to the other you can create a difference from the expected value.
So what happens if you remove the Rzero resistor and use a lower PGA gain? The negatives is the noise may increase a little and the dynamic range is lower which may reduce the resolution, but the positive is with a reduction in drift, and the simpler calculation.
Whether you use the Rzero or not is up to you. In most designs we've seen the Rzero resistor is not used, and is only usable with a 3-wire RTD.
Best regards,
Bob B