The character of Orolo observed it for a while and explains that he
believes that the ship is not send from another star system because it
is too small and slow to make that journey and therefore it comes from
a different universe.
It would help if you could provide this quote, because it doesn't match what I see in the book. Orolo, shortly before his death, declaims his knowledge of the ship:
"I remind you that I was Thrown Back before I saw the last picture
that I took of the alien ship."
"Of course. But I assumed you had taken other pictures before then -
had been taking them for a long time."
"Streaks and blobs!" Orolo scoffed. "I was only learning how to
capture a decent image of the thing."
You may be thinking of Barb's commentary on the ship, instead:
"A piece of the PAQD ship is missing!" Barb announced.
"That structure you've been studying - "
"It's where the missing piece used to be attached!"
"What do you think it was?"
"The inter-cosmic transport drive, obviously!" Barb scoffed. "They
didn't want us to see it, because it's top secret! So they parked it
farther out in the solar system."
But that's all conjecture on Barb's part, not backed by anything else we find out in the book. We never get other mention of it, but since we know that the PAQD dropped capsules onto Arbre to infiltrate the Matarrhite's Concent, that's a likely explanation for the missing equipment.
It turns out he is correct about his conclusions
Again, not sure which conclusions here, but it's not necessarily correct that the Daban Urnud isn't sized correctly to do what it was designed to do - travel between solar systems within a single narrative. And in fact, in the home Narrative of the Urnudans,
[The Daban Urnud] was designed to send a colony to a neighboring
star system, only a quarter of a light-year away.
It simply hasn't done so because they keep crossing narratives instead of going somewhere in one narrative.
"The first Gan of the Daban Urnud was entrusted with the
responsibility to establish a colony on another star system," Gan Odru
... "Late in [the third Gan's] career, he became aware of your
summons, and made the decision to alter the trajectory of the Daban
Urnud so that it would - as he conceived it - fly into the past."
And when they do cross narratives, they seem to show up near planets, bypassing the interstellar aspect upon arrival:
"But when they reached the end of that journey, they found themselves,
not in the past of Urnud, but in an altogether different cosmos,
orbiting an Urnud-like planet --"
"Tro," said Arsibalt.
"Yes. This is how the universe protects herself - prevents violations
The ship apparently left its version of earth using its nuclear pulse
drive and completed a journey around the entire circumference of the
universe which leads to the same place but in the past.
Anathem never suggests they circumnavigated the universe, and given the number of years they've been traveling - roughly a thousand - we know that's not possible, since the most they can do is relativistic velocity.
The only technical specification we get is that they be able to travel far and fast enough:
"Geometrodynamics!" said Suur Moyra.
"If the equations of geometrodynamics are solved in the special case
of a universe that happens to be rotating, it can be shown that a
spaceship, if it travels far and fast enough --"
"Will travel backwards in time," said Paphlagon.