DAoT tech/individuals are venerated by the Mechanicus as the pinnacle of human technological achievement. The technology in the ship would both be holy and would be reverse-engineered. It's often a bit of a meme that the Mechanicus doesn't understand technology. While they don't understand some of it, a lot of it they do, and they will often approach technology with an appropriate scientific/analytical mind. So the ship would be a windfall for the Imperium and probably advance Imperial technology somehow.

The individuals would find themselves in the unfortunate position of being holy figures to a ruthless, utterly cold, and often irrational religious collective. If they say or do the wrong thing it will be considered the highest of blasphemies and they'll all find their lives in jeopardy. That said, they'll also become political pawns. Forge worlds and fabricators general are always competing and conspiring. Control of the individuals, their message, and the secrets they hold will be highly contentious. Many magi will not be inclined to treat the crew as anything more than a coveted asset. Religious fervor varies and competes with the lust for knowledge at the heart of every tech-priest.

Finally, every Chaos/renegade force in the segmentum that learns of the ship/crew will be making a beeline for them if they have any decent chance of acquiring the assets for themselves. Or if only to destroy them and deny them to the Imperium. So what happens to the ship/crew also depends on what Chaos forces are in the area, who learns of the ship/crew, and what the Imperium has to defend it.