Adding a comma when "setting the scene/state" in a sentence

It has been my understanding that, when "setting the scene/state" in a sentence, even if doing so after the word "that", it is good grammar/punctuation to use a comma to delineate this:

This means that, within the scope of the program, we have high levels of complexity.

This means that within the scope of the program, we have high levels of complexity.

As can be seen, we can even apply this to my first sentence of this question:

It has been my understanding that, when "setting the scene/state" in a sentence, even if doing so after the word "that", it is good grammar/punctuation to use a comma to delineate this.

It has been my understanding that when "setting the scene/state" in a sentence, even if doing so after the word "that", it is good grammar/punctuation to use a comma to delineate this.

It seems to me that adding the comma "modularizes" the sentence and, in a way, adds clarity. However, it is relatively common for people to not write like this. So is it better gramamr/punctuation to write like this (that is, to include the comma), or not?