How is this comma usage explained with Thomas Pynchon?

"They move slowly, without resistance."

has nothing to do with "non-essential phrases". The comma you see is a "pause comma", the author is showing you how to say the sentence.

They move slowly, coldly, without resistance, toward Mittelwerk.

These are "list commas" the adverbs qualify the verb individually, rather than each other.

Given that this is a literary example, we can defensibly presume each word and punctuation mark is intentional. The original sentence and the two alternative versions you give would also be acceptable constructions, so we can assume there's a reason to use one over the others.

As for the comma, it's likely doing something more than telling the reader how to pronounce the sentence, unless we're looking at an instance of a character speaking. Typically (though there are of course many exceptions), the narrator isn't a character and so the narrator's "voice," including features like pronunciation or prosody, isn't what's coming through by way of punctuation. In narration, as opposed to characters' speech, punctuation (along with all linguistic and orthographical features) is presumably intended to affect the reader's interpretation; in cases of ambiguity, an intended effect could be to evoke in the reader one interpretation over and above other possible interpretations.

So, if we take the alternative examples you give, we could ask whether there are different possibilities for interpreting the three versions, and this might suggest why the author made certain punctuation or lexical choices. Of course we can't really know why the author did one thing as opposed to another, and below are just my own offerings of possible alternative interpretations, but they demonstrate my overall answer, which is that literary usage of punctuation is related to authorial intention and the (always present) possibility of differences in reader interpretation.

They move slowly, without resistance.

This is essentially a serial comma. We might interpret this as: "They move slowly and [they move] without resistance."

They move slowly but without resistance.

Without the comma, this feels similar to the above. "They move slowly yet they also move without resistance."

They move slowly, but without resistance.

The work the comma does here is subtle, but my suggestion is that it makes explicit the relationship between slowness and resistance, and specifies that the relationship isn't causal, as in: "They move slowly but their movement isn't slow because of resistance."