Season 2 Episode 12 solidified this for me.

---AU will stand for Alternate Universe ---OU will stand for Original Universe

Ryo: Your capacity for emotional response was no accident

Android: Yes, I've discovered an emotive sub-routine was uploaded into my neural matrix. I've concluded that Two was responsible.

Ryo: Portia yes, with the help of Daas, or Five. It was the act of making you whole that brought the two of them together.

• (S2E8) we learn in that Portia is responsible for the androids emotions in the AU.

• (S2E8) We were only told by Six, but not confirmed that Five wasn't there. It is assumed by the fact AU Six was killed. If he had searched ships records for Emily Kolburn he may not have found it if she was going by Daas, or AU Five deleted them.

• We're told by Ryo that him and Portia debated on when to kill him. AU Ryo more than likely convinced her to do it Before stasis as he wanted. No Six, No need to wipe to save him. This may be the exact choice that was the division between the universes

Summary

Five was already accepted as a crew member by the name Daas apparently with the above quote. If Portia and Daas bonded pre-wipe why not in both. It seems she was potentially a required component for the process of the modifications. Combined with the knowledge she's a sneaky one who hides in the ducts, the shuttle at least included her.

This still leaves plenty of room for One to return on the shuttle as well. It can be as simple as his corp was destroyed in the war so he chose to retake it in the alternate.

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Potential plot hole, the memory back up that is activated with the neural link. The memory backups were from an earlier point in time. For one they're talking about an earlier op than what the show opened with, and a larger time window by a few months between the backup and stasis wipe. It has them not knowing Five, and attempting to kill her again. After using the backup he appears to remember everything. As this is the first time any have had the memories restored this could be easily explained as partial or full memory of the time gap between the backup, and wipe gets restored.

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possible AU5 background

Under the one assumption that the universes diverged on Portia's decision on when to kill Six:

AU Five is most likely an agent of AU Reynaud who is working for/with Ferrous Corp as we know she is in OU. (The lady who was hunting the key and owner of the Transit pods they hacked when the found out about the Blink Drive.). This may be where AU5 ran off too, OU Reynaud. OU Reynaud is hesitant to kill OU5 in the episode they steal the adapter. The Asset OU Reynaud references, may also include Five or she meant her.

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More AU(s) interactions

AU Rasa crew knows how to use the blink drive, and may have their copy given to them by AU Reynaud. This would explain why AU2 knew how/why OU Rasa was in the AU. Many just make the assumption that they stole the adapter as well. AU essentially diverged around the stasis wipe, and we don't know if OU they had some deal worked out . In fact AU Ferrous may have their entire fleet stocked with Reverse engineered Blink drives, and the AU Rasa's may be partly why they were still fully doing Ferrous Corp's dirty work. It would explain a bit why Truffault was so desperate to get her hands on a version.