I think this is up to the end user (bettor).
Personally, when tracking a 'systems' performance, I think all plays that meet the system parameters (RPI and filter criteria) are in play and count towards the final performance.
A 'system' should be automatic so that any monkey can press a button to use it. When you start handicapping your system, it is really no longer a system that anyone can use because everyone will handicap differently and thus have different results.
IOW, it's my thinking that all four plays today should count towards the performance statistics of the system. Whether or not you personally play all four is up to you.
Good points. I think for the Dodgers I'll still play it but maybe 1/2 unit instead of full. I did the same for the White Sox the other day.