There are a number of ways of understanding קם ליה בדרבה מיניה. There are actually different opinions that are presented and explained.
A very simple and straightforward way to understand it is as follows:
It's not that we only give the person 1 punishment for 1 act, and not 2 punishments for 1 act. Because then the question is "why not?". If a person stole on Shabbos and he did it in 1 act, why should he only be חייב מיתה for being מחלל שבת and not have to pay for the stolen item.
Rather, we say that we only see the more severe עבירה and therefore naturally he will only receive 1 punishment.
A simple way of demonstrating this logic is to use the example of a person killing another person by stabbing him in his heart. We won't say "he ripped his shirt and killed him". One may say that's an absurd statement. Rather all we say is "he killed him" and therefore naturally he only receives 1 punishment.
In other words, if we saw 2 עבירות there would absolutely be 2 punishments even if it's all in 1 act. But in such cases we only see 1 עבירה and therefore naturally there is only 1 punishment.
There is a תוספות in בבא קמא that discusses this. ריב"א says there that we DO find 2 punishments in a case where a person's ox that's a מועד to kill. If he killed another person, both the ox is killed and the owner must pay כופר. This is because we only see 1 עבירה and that 1 עבירה has 2 punishments. So we see that a person is able to receive 2 punishments for 1 act, but only when it's 1 עבירה, but not when it's 2 עבירות.
This is my first time on this site. I was looking for something and it came up right on top.
Best to all