I can not discern any of the words from the calligraphy. Was this intentional? Is this just my modern ignorance? Or did the literate person of the day simply learn throughout their whole life that that was how letters were written.

I had to do paleography during my PhD, and this kind of text is readable, it just takes an awful lot of practice to get used to. The added complication to modern eyes are the added abbreviations and contractions to the Latin thrown in by the scribes which make it all the harder to discern what letters logically follow on. To scribes trained in this script from an early age, the style would be far more readily recognisable.