The X have acted as a means for Samus to absorb new powers ever since Fusion, that's the entire concept behind the Core X. Metroid is one of those sci-fi settings where genetic information is also encoded with experience, memories, abilities, etc. And Metroids change, genetically, based on what they eat! Does ti make sense? I mean, not really. But it's been like this for about 20 years, so it's not new
With regard to Quiet Robe reactivating the E.M.M.I.
I think it's worth remembering that the Chozo are psychic, and in fact have always been psychic. It allows the Thoha to control the Metroids, it meant that the Thoha weren't immediately attacked by the X on SR-388, it's how Mother Brain controls life on Zebes, and it allows Raven Beak to control the X!
And yes, it's subtle, but Raven Beak does control the X. It's why the X-ified Chozo Soldiers still obey him and specifically act as his guards. The other possible explanation is that the underlying consciousness of the guards persists, but the two aren't mutually exclusive, either
The way I see it, there's two possible explanations for why Quiet Robe would reactivate the E.M.M.I.
1. Between Quiet Robe's death and resurrection, things have changed a lot. Samus is going to need the power that each E.M.M.I. houses, so even though it's going to be dangerous, the only way to force her to interact with them is to wake them up and put her into direct conflict with them
2. Quiet Robe was under Raven Beak's control when he did this, and behaves differently in the ending because Raven Beak lost control of the X—including Quiet Robe—when Samus grabbed hold of him and destroyed the information network. So at about the same time an X decided it was time to absorb Raven Beak (some time before it actually happens!), Quiet Robe would have also been freed from that control, and rushed to help Samus
Either explanation feels cogent enough to me