I relistened to the sequence from the point the Mallers blew up the other tanker with the RPG to after Angel pulls Riley from where ever she got knocked out from. What it sounds like to me is you're hearing Burt cough if you're talking about the next immediate human sounding thing after Angel says "where are you." I listened after that for anything else that sounded like a laugh but I didn't hear anything that could be a laugh.
But just to be sure: You're talking about the two distinct low sounds you hear just before Burt speaks again, correct?
Now the howl that was heard about 40:25 could have been TOWTM, or it could have been any Smart One with the capability of communication.
I first listened to the season finale immediately after hearing Episode 23 (The Devil's Workshop) Part 3 and something about that sound really resonated with me. It sounded just like the One with Markings' laugh. You know, right before Riley shot him with the arrow (5:16). That devious laugh reeked of one intending retaliation and then here's the same "laugh" again as Riley is calling for help.
Since your post, I've relistened to that scene over and over again. Sometimes I hear it as Burt coughing and sometimes I feel it's definitely the One with Markings laughing. It's so hard to say, especially given all the background noise of the Tower failing, guns firing and stair climbing.
You'll notice a lot of people will use the names interchangeably, depending on their personal preference. In this thread, I was specifically thinking of the one Kalani and Riley encountered at the Hospital, who we heard laugh.
I'm probably alone in thinking I heard the laugh again in this chapter. But then again, my hamster has the same evil laugh, so it might just be me.