Anglicanism was coined to describe the common religious tradition of these churches; {as also that of }the Scottish Episcopal Church, which, though originating earlier within the Church of Scotland, had come to be recognised as sharing this common identity.
2 Answers
It's an abbreviated reference, to save having to say the same thing twice...
Anglicanism was coined to describe the common religious tradition of these churches; as also [(to describe) the common religious tradition] of the Scottish Episcopal Church
that = relative (anaphoric) pronoun referring back to an earlier noun or noun-phrase
as = in the same way, similarly
also = in addition, as well, too
and also too that [i.e. the common religious tradition] of the Scottish Episcopal Church
Compare:
This "Renaissance" of the Latin language (as also that of ancient Greek) did not start any earlier than the 8th-9th century.
as also the "Renaissance" of ancient Greek...
and the "Renaissance" of ancient Greek as well