looking for the intent of the rule....

[officialtony]

I think the intent here is to prevent the offense from intentionally interfering so a run can score - perhaps a game winning run.
If you call out the runners on 1st or 2nd, and the runner going home is allowed to score, you have rewarded the offense with a run - and only trading an out for the run. Coaches might do that in a close game knowing they could get a run for an out automatically.
Again, what if is tied in the bottom of the 7th, bases loaded and 1 out. Everyone is on the move ( knowing the coach has " the play " on ) and the batter interferes. By calling anyone out but the runner coming home, you have essentially rewarded the offense with a win for an illegal act.
This is my take on the rule reasoning for calling the runner headed home out.
I could be way " off base ".