I am not sure what manner of parasite it most resembles- that sort of thing can be deceptive. Roundworms often resemble spaghetti, but tapes can come in segments like that, and flukes can also kinda look like that. There are definitely some species of insect larvae that look like that as well. I’m honestly shocked that your vet didn’t request a sample to slap under the scope- though perhaps it was very obvious to them that they were fly larvae. I’ve had it happen plenty of times where I instantly recognized various parasites upon discovering them.
I have a theory (I’ve already had my evening pain med, so it might be totally zany):
Mammals of various species can have issues with improper closure of umbilicus/belly wall/liver/even bladder. I’m most familiar with this in horses, so I’m rusty, as I haven’t worked with equine med since 2015. If you google “patent urachus” (be prepared for medical images and descriptions), it will explain some of it better than I could.
Now, I know reptiles have a coelom instead of a separate chest and abdomen; their development and anatomy are way different. So I don’t know if this could possibly be an analogous condition, as there’s a yolk instead of a placenta… They did not teach much about reptiles at my vet school, unfortunately. 
Another thought would be as mentioned, that there wasn’t full closure of the belly wall- that might be the more likely of the two.
Though, and this is a totally wild guess (and I am out of my depth in terms of reptile medicine), mammals can contract tapeworms from ingesting rodents that are infested with fleas. It’s why indoor cats that are on flea preventative, but are rodent hunters, will still constantly get tapeworms. But that strikes me as way less likely than an external parasite infesting vulnerable tissues.
Whether my thoughts were on target or way off base, I wish your baby a smooth recovery! I’d very much like to have updates as well, if you have time.