A whole lot of what you see in the "Lost Scene" is retconned into the thing to establish more continuity within the Askewniverse.
Alyssa. "Finger Cuffs." Truth or Date. T.S. Quint. The images of Loki and Bartleby on the death announcement cards for Julie Dwyer. Which is all cool and it never bothers me. It's not as if Kevin knew who or what any of those were in the winter and spring of 1993 when he first shot the original Clerks, and it only helps flesh out his universe and gives it more depth.
If retconning works, I say go ahead and do it.
While you're right, the majority of it is retconned, I did make one mistake. Alyssa was a character as of Clerks, at least in passing. Heather mentions her when telling Dante who she is. Ah Heather Jones, one character we never saw again, I would have liked to see her exiting the theater with Trisha and Alyssa.
Anyways, I just watched Clerks. As I've mentioned many times before in this thread, for me the View Askewniverse begins and ends with Dante and Randal, they are the two best characters that Smith created (outside of Jay and Bob), and any chance to see them in something new is a joy. Along with the movie I did rewatch the "lost scene" and also watched the short film "The Flying Car" which I remember watching back when it premiered on The Tonight Show.