The same fan/shroud setup generating different airflow through the different radiators is very likely. It is also a real world factor that needs to be considered when looking for "the best" radiator. Same for coolant flow. All other things constant, a radiator that can flow more air and water should have an advantage that will be reflected in the temperature drop. I am assuming he will also be looking for "the best" fan and water pump, which is beyond the scope of this question. Also assuming they are the same or very similar physical dimensions.
Comparing apples to oranges is fine in a number of scenarios. If you want to fit the maximum weight of fruit in an existing crate, you aren't going to check apples in one size crate and oranges in another. You're going to fill the crate with apples, put the lid on, weight it, then do the exact same with oranges. You're not going to change the dimensions of the crate from one fruit to the other.
Check idle conditions (fan only for airflow, water supply characteristics to emulate waterpump curve at idle engine rpm) and see which is best. You may be able to simplify things even further if you can maintain constant ambient temps. I assume the main objective is to avoid overheating at idle? Run a closed loop water system and log the temp rise until stable, and what the max temp is.
If this is for a research paper on radiator design, instead of a real world application, ignore these comments.