I think because the book Killer Angels followed Chamberlain and the 20th Maine, the movie would also follow them, even on Little Round Top. So most of the action on the 2nd day isn't covered in the film, and only the 20th Maine section of LRT is in the film, where trees actually were, and still are. The treeless rocky slope you're thinking of involved other Union regiments closer to the front of the hill. I think because it would've been very difficult to recreate or find another location of the treeless face of LRT, where a lot of Rebs attacked, they didn't film the whole fight on LRT. There are a ton of paintings out there that will give an idea of what the fighting looked like.
The only part of the film actually filmed on LRT was the next morning, with Chamberlain "resting his leg," and his brother Tom bringing him coffee. Then another scene which a courier informs Chamberlain that he is relieved from LRT, and he's been relocated to a "safer spot" on the battlefield. That was filmed on the treeless rocky slope, which ironically, Chamberlain didn't fight on that part of LRT on day 2, and wasn't left in place there. He actually was stationed on Big Round Top, so the courier should've came to him on BRT, not LRT, and especially not the wrong part of LRT! So again ironic, the courier scene should've been a wooded area, since Chamberlain was on BRT, not LRT, and it was completely wooded. Also a fun fact: that courier actually played Gen. Pickett in God's and Generals
I know a guy who lives in Gettysburg, he was Reb charging up LRT in the film, I asked him about the location of the filming of LRT, he said it was outside of town not far.