It is not clear to me that this usage needs explanation. That is, using "Mr X" to refer to a rector in early 19th century England was not unusual, and was not disrespectful. In Anthony Trollope's 1858 novel Doctor Thorne the character Caleb Oriel is first mentioned in
Then there were the Bakers, and the Batesons, and the Jacksons, who all lived near and returned home at night; there was the Reverend Caleb Oriel, the High-Church rector, with his beautiful sister, Patience Oriel; there was Mr Yates Umbleby, the attorney and agent; and there was Dr Thorne, and the doctor's modest, quiet-looking little niece, Miss Mary.
This is the only use of the word "Reverend" in the book.
Thereafter he is "Rev Caleb Oriel", "Mr Caleb Oriel" and "Caleb Oriel" once each, and plain "Caleb" 8 times. But he is "Mr Oriel" 88 times, in quoted speech addressed to him, as in
"Ah, a bore!" said Miss Gushing, in an enthusiastic tone of depreciation. "How insensate they must be! To me it gives a new charm to life. It quiets one for the day; makes one so much fitter for one's daily trials and daily troubles. Does it not, Mr Oriel?"
and speech not addressed to him, as in
"It that so odd?" said Mary. "You love Mr Oriel, though you have been intimate with him hardly more than two years. Is it so odd that I should love your brother, whom I have known almost all my life?"
and most often, by the narrator, as in
Now Mr Oriel was a modest man, and, when thus addressed as to his future wife, found it difficult to make any reply.
Austen's and Trollope's characters are social equals: the sons and daughters of gentlemen. They must have spoken pretty much the same language and followed the same social usages, even though they are separated by almost fifty years. Austen and Trollope are, in effect, anthropologists describing the same tribe. Neither reports extensive use of the epithet "Reverend".
So an answer to the question "Why is Mr William Collins never referred to as the Rev Mr Collins in Pride and Prejudice?"
the answer is "why do you think he should be"?