Manually opening pesterlogs provides a beat between seeing the panel and reading the log beneath it, and this beat is used for dramatic or comedic effect.
For a comedic use, peachy comes to mind.
In the original comic, the pacing of the joke is "I FEEL SO GREAT!" (beat as you go to next page) "I FEEL SO ALIVE!" (beat) "I FEEL SO..." (beat) (see fruits) (beat) "PEACHY". Without the extra beat of opening the log, "PEACHY" immediately grabs the eye, and the punchline arrives before the joke is fully told. There's no moment of confusion over seeing the fruits before the punchline because you only register them after your eyes dart back up from the log. The joke is not given time to breath.
A more dramatic example is on this page: https://homestuck.com/004163
On the original site, there would be a pause as you registered what's happening in the panel, then you click to open the log, then you're surprised when you see doc scratch talking in the text sparking with electricity. Wow, animated gifs in the pesterlogs? Huh. Neat.
Without that pause, the experience is flattened in my opinion. An example with Jade will be coming up later as well where opening the log makes for a more enjoyable surprise than just having it all happen on-screen at once just by going forward a page.
Edit: that page has now released (https://homestuck.com/004907)
The experience would be better, I think, if a reader could open that and be surprised -- a gift to unwrap -- rather than just being there immediately.
And later on, when the buttons are broken [1] and the narration talks of being unable to open the log, I think the moment lands better when you've actually had the experience of opening the logs at some point during the course of the comic. When the buttons default action is to show the dialog, it makes sense that the button being broken prevents you from being able to see it; that's what the button does: shows the dialogue. Gosh, I sure wish the button worked so I could open the dialogue! When instead the default action is to hide dialogue, it's just suddenly the case that a button that's primary purpose for hundreds of pages was to hide the dialogue now does the opposite. Or would, if it weren't broken. I think it's entirely conceivable that someone would not have pressed that button a single time during the comic, but now they have to make the association that that button (one they've barely registered) being broken is why the dialogue is hidden.
I get the impression these sorts of details (not all related to Homestuck) matter more to me than they do to most people, but they do matter to me. So while I do earnestly believe that opening the logs automatically is an artistic harm for the sake of a convenience gain, I fully expect the convenience gain to be more important to the developers of the website; they did develop the site that way, after all.
So, if changing the behaviour to align with the original experience of reading the comic is not on the table, a user-preference to get back the original behaviour would be appreciated.
Thanks.