The same rights of reciprocity were extended by the King of Spain to Protestants provided they did not do or say anything offensive to Catholics in territories ruled by Catholics.
Whatever the many and varied reasons why the Boston Pamphlet would exclude Catholics from the pale of full religious tolerance, it's more likely that as part of the British Empire at the time this was a rhetorical tip of the hat to the moral authority, if nothing else, of the Treaty of London that opened up the New World for development and settlement by all Europeans.
I'm sure more than a few Colonials had read that Treaty.
I did a few months back ~ the whole thing, plus all the codices ~ and I'm impressed with the wisdom of King Philippe II/III and his counselors in coming up with this path to peace.
Lasted 20 years which was really something back in those days.
I'm sure the rest of the Americas still held by Spain, or which had formerly been held by France, really weren't all that upset by the continuation of the exclusionary clauses.
I read an article about the Stono rebellion in South Carolina in 1739 which argued that the slaves were Catholics (captured in the Angola region) and were trying to get to Spanish Florida.
I think the notion of toleration for Protestants of different types, but not for Catholics, may be drawn from John Locke's essay on toleration, written about the time William and Mary extended toleration to Protestants in Britain (although there continued to be disadvantages for non-Anglicans).
One of the reasons for the intensely negative reaction to the Quebec Act of 1774, I think, was that it gave rights to the French Catholics in Canada. Of course they also didn't like the enlargement of Quebec to include the land north of the Ohio River.