I think the main thing with say Syrian Rue for example compared to Caapi is that people generally don't seem to work with the Rue thoroughly enough, especially by getting up in the heavier Harmala dosage territory, the thing with Rue is you don't wanna take over 4 grams of Rue because 4 grams is plenty strong enough, but taking 4 grams daily or a few times a week allows you to build up the Harmala reverse tolerance and it takes you deeper into the Harmala territory, one can also do this with Harmala extracts as well. But as you get up in the Harmala dosage, effects start to come out that aren't really there in lower dosages. With traditional Ayahuasca, they tend to go heavy on the Caapi, whereas with Rue one can only take so much because it's much more potent and the background compounds definitely can make things uncomfortable compared to Caapi. But the Spirit of Aya is in the Harmalas, and that applies to Caapi, Rue, other Harmala-containing plants, as well as Harmala extracts. When most people dose Rue or Harmala extract, they don't have as much compared to what may be in a traditional Caapi-based Aya brew.
With that said, the background compounds of the plants do contribute and make up the personality/characteristics of the plant, or what some folks see as the "spirit" of the plant, and so of course one plant will be different from the other in terms of how it feels and some of it's effects and it's personality, but the Spirit of Aya is in the Harmalas and can be accessed through Caapi, or Rue, or extracts, ime. Though the background compounds are often times a desired component as Harmala extracts ime/to me feel more isolated and i much prefer a more full spectrum synergistic feel.
Personally i use Rue, been taking it for 12 straight years on the daily/near daily, with some extracts or Caapi here and there, i find i like the Rue personally more than Caapi, but Caapi is nice too, Rue just has more going on compared to Caapi. It doesn't matter what i use though, it's all Harmalas and DMT and as such i get the same results either way, just flavored differently.