What is the Roman Catholic Church doctrinal justification of its perceived opposition or support of the independence of Catalonia?
I do not believe that this is a clear doctrinal subject matter at all.
This seems to be a of some sort private political statement, as it comes from the pope speaking to Spain's new ambassador to the Vatican at his accreditation to the Vatican. This in itself, indicates that this is indicative of Pope Francis’ personal political policy and is not a doctrinal issue at all.
This is most evidently a political and not doctrinal aspect at all, as Pope Francis clearly states that “the Holy See is against all self-determination moves that are outside decolonization processes.” The title of the Holy See is employed officially for diplomatic reasons of Vatican City.
Although the Holy See is sometimes metonymically referred to as the "Vatican", the Vatican City State was distinctively established with the Lateran Treaty of 1929, between the Holy See and Italy, to ensure the temporal, diplomatic, and spiritual independence of the papacy. As such, papal nuncios, who are papal diplomats to states and international organizations, are recognized as representing the Holy See and not the Vatican City State, as prescribed in the Canon law of the Catholic Church. The Holy See is thus viewed as the central government of the Catholic Church. The Catholic Church, in turn, is the largest non-government provider of education and health care in the world. - Holy See
Traditionally pope welcome new ambassadors that are accredited to the Holy See when they present their credentials (The Credential Letters of the Ambassador of Spain to the Holy See, 02.10.2017) and Pope Francis, I believe was pointing out a few personal observations at this moment in time.
Many may be confused as to what business the Catholic Church would have in supporting or opposing an independence movement, but it may simple be that of the Pope‘s personal views being expressed here. This is more evident as it is simply a statement on the at the moment H.E. Mr. Gerardo Ángel Bugallo Ottone became an ambassador of Spain to the Holy See.
Even the linked article itself points out that the pope was speaking to the new accredited ambassador to the Holy See and did not issue a doctrinal statement through the Congregation for the Doctrine of the Faith.
This is, in fact, a very complex question to answer due to the fact that the Vatican's Secretariat of State (Dicastery of the Roman Curia) is divided into two sections: the Section for General Affairs and the Section for Relations with States. As the supreme leader of both a country (Holy See) and a world religion (Catholic). The Vatican does not have to have a doctrinal justification with the Catalina issue. This is a political question and would be dwelt within the Section for Relations with States.
As for the 400 hundred priests supporting its' independence this could very well be a personal opinion of Pope Francis. I see no doctrinal issue involved in this subject matter, at least none have from forth from the Holy See and doubt any will be forth coming.
Historically popes has been involved in political issues of one nature or another for a variety of reasons. Foe example, Pope John Paul II negotiated peace between Chile and Argentina in 1978. This was all done through the diplomatic channels of the Holy See (Section for Relations with States) and was in no way a doctrinal issue at all.
It would also be beneficial to this subject matter if we had the exact words pronounced by Pope Francis himself, without a third party interpretation!