To answer your last question, yes you can use intersample calculations across result sets but you have to set it up to suit your needs, can you be more specific about what you are looking for?
You also need to specify the search order of your custom field to either "Outside First" or I suspect for your needs "Result Set First", that way it starts the search in the current result set and continues outside. Be aware though that an intersample calculation only targets ONE result if your search order is set to "Result Set Only"and, for example, if you wanted [S01.2.(Height)] and it finds this in the current result set, the search stops. If you don't process a sample set or process from Injections/Channels, the "Outside Only" is your best option.
For example, and I am just pulling this from thin air, lets say you want the area of a peak in a sample injected multiple times divided by the average area of the same peak over multiple result sets, you need 2 CFs linked into 1. Firstly, label your sample injections the same eg SAMPLE Your intersample CF looks like: SAME.%.(Area).
Second CF calculates the average area as per SAME.%..Average(Area).
Tie them together as per (SAME.%.(Area)/SAME.%..Average(Area)) Peak Real and Calculated. Select relevant result sets, view as peaks and set up a View Filter to see the results of the custom field. Best of luck.