I have to admit that I was very thrown by your question. I've read Krakauer's account of Chris McCandless, and I know that Corinne McCandless has published a book that details her interpretation of Chris and what happened to him; however, I did not know that any book about McCandless had been written by a person named "Penn." Then I remembered that the 2007 movie was directed by Sean Penn, and the screenplay was also written by Sean Penn. I am going to assume that is the "Penn" that your question is referring to.
I'll start with this. I really enjoyed Krakauer's book. But there were parts of it that really annoyed me as a reader. I didn't like the constant flashback interruptions, and I didn't like the break from McCandless for two entire chapters while Krakauer narrated about other men that McCandless was similar to in various ways. I understand what Krakauer did, and I appreciated the comparisons, but it still annoyed me a lot as a reader. I like chronological story telling. I understand the concept of flashbacks, but I usually don't enjoy them, because it always seems that the story is being broken and new plot lines and characters are being introduced.
So for me as a reader (and in this case movie watcher), I preferred Penn's more chronological story telling. I do want to note though that Penn's narrative wasn't free from flashbacks. His movie and screenplay starts the same way that the book started. It started with McCandless being dropped off a few months before he dies and then flashes back to the sequences mentioned in your question. I more enjoyed Penn's focus on McCandless as a singular character and showing his journey in a relatively unbroken narrative. For viewers and readers, I think Penn's version is more accessible than Krakauer's version.