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.

There are two known versions of this poem Tête de faune by Rimbaud, the version you refer to, with a comma before se recueille is from a manuscript by Rimbaud.
The version published in les Poètes maudits has no comma.

I personally do not think the place of the comma changes the way we should interpret this line but I agree with Maroon’s answer saying that it is the Baiser d’or who is the subject of recueillir.

My own interpretation of the poem is that Le baiser at the start is asleep (le baiser dort, line 3). While the baiser (to me it personifies the poet but other interpretations are possible of course) is asleep the faun arrives and kisses the red flowers. Amidst the faun’s intervention the baiser – who by the last line of the poem is referred to as le Baiser d’or – remains asleep, or at least half asleep (→ il se recueille).

But as I said other interpretations are possible as this one given here :

Suite à [l’acte du faune], le bois se pâme dans une longue extase (dernier vers : « Le Baiser d’or du Bois, qui se recueille. »)¹

¹ After the faun has perpetrated his act the wood swoons into a long ecstasy (my translation).