Syntactically, "which" has several possible antecedents, and which of them is intended is a question which has to be determined semantically. In other words, in this case we have to decide what might be further promoted by common currency.

Of course, the first option one considers is the immediately preceding noun, "incentive". But it is not likely that one would speak of "promoting" an incentive, and besides, a common currency would probably involve common regulation, so it would not coexist with and promote larger differences in regulation.

Another possibility is that "which" refers to the fact that FTA agreements promote cross-border deposits, but what is said previously suggests that when there is a common currency FTA agreements have little effect, so it is not likely that the author means that a common currency promotes the effect of FTA agreements.

I think the likeliest reading is that "which" refers to cross-border deposits. The sentence is saying that these are promoted by FTA agreements and can be further promoted by a common currency: a common currency is more effective than FTA agreements in promoting them. This is consistent with what is said previously. The use of the same verb, "promote" suggests that this is the essential parallel: that "cross-border deposits" is the effective object of "promote" in both cases. So "possibly because [...] act as an incentive" is a lengthy parenthetical phrase inserted between "which" and its antecedent, "cross-border deposits".