This question, Google Ngrams, Wikipedia, and several dictionaries all say that connexion is an alternate, obsolete spelling of connection.
I am reading a several-hundred page treatise (Milton S. Terry, 1890, Biblical Hermeneutics), wherein the author uses both forms, favoring connexion considerably. The instances of connexion (84) are listed here, and the instances of connection (9) are listed here. I think what I am reading is the author's 500-page condensation of the work linked.
My question is this: Why is connection used at all?
Does it really mean something different? It appears to be used synonymously. Is it merely an instance of non-standardized spelling (as with the diaries of Lewis and Clark, where a word can spelt multiple ways in a very short space)? This would be the only instance of this that I have found so far. Is there a different explanation that I haven't yet considered?