Analysis of this sentence and the "through via" usage within

Solution 1:

Through and via are both prepositions, but they are not used together.

To come through is indeed a phrasal verb:

If something comes through, it arrives, especially after some procedure has been carried out.

• A huge cheer of relief went up when the result came through. (Collins)

If you replace this phrasal verb with a synonym such as arrive, you get:

Automatic encryption of all traffic arriving via AWS global and regional networks.

Via is defined by Cambridge as

using a particular machine, system, or person to send or receive something; by way of, or by use of:

• Reports are coming in via satellite.

In this example you can see another instance where the preposition of the phrasal verb is juxtaposed to the preposition via that is linked to the noun "satellite".

Though these two prepositions stand next to each other in the sentence, they are linked to different words. This is not the case of compound prepositions connected to the same word (Your dictionary) as in:

He picked up the penny from beneath the couch.

Edit: Prompted by a comment, I will add another source for a compound preposition, though I am not sure it is more "suitable":

He didn't go to university because of his grades. (Advanced English Grammar)

Neither is this a phrasal verb with two particles which is called a three-part phrasal verb, such as:

go through with = to do something you promised to do, even though you don’t really want to do it:

• She went through with the wedding, even though she had doubts. (English at home)

Solution 2:

There are legitimate objections to some aspects of the full passage quoted, but not to the particular pairing.

The first preposition is, in effect part of the verb 'come through'. It behaves as a kind of 'suffix' to the verb 'come' (classicists might describe it as 'enclytic' - literally 'leaning back'). The second, via, is a straightforward preposition, literally 'placement before' the noun that follows.