This is something that is determined by context. Relative pronouns such as qui can modify an entire phrasal noun or just part of it. Some examples taken from « Les Chansons de Bilitis » :
« Je te bercerai d’une main sur mon genou qui se lève et s’abaisse. » : The relative clause is clearly attached to « mon genou » and not « une main sur mon genou » by context.
« Quand aurai-je comme toi des seins de jeune fille qui gonflent la robe et tentent le baiser ? » : The relative clause is clearly attached to « des seins de jeune fille » and not « jeune fille » as the verbs are conjugated in the plural. The « jeune fille » is also by context an inappropriate subject for the verbs.
In this example from Rimbaud, « se recueillir » probably refers to « le Baiser ». This is indicated clearly in the translations of the poem that I found while looking for references:
And the Golden Kiss of the Woods, started by a bullfinch, resolves once again to rest. (Mason)
And one sees frightened by a bullfinch the Golden Kiss of the Woods, communing with itself. (Ahearn)
… and you can see frightened by a bullfinch the golden Kiss of the Woods, in meditation. (Appelbaum)
One might also observe that in the clause, « le Baiser d'or du Bois » is already treated as a unit by « l'on voit épeuré ». Because of this precedent and the comma, which implies a pause to me, « qui se recueille » probably also applies to the entire phrasal noun. If it were instead attached to « le Bois », I would expect it to more or less proceed without a break, to make the attachment clearer.
et l'on voit épeuré par un bouvreuil
le Baiser d'or du Bois, qui se recueille.