What input connector are you using during this "4:3 on a 16:9 screen" mode switch? Also, have you actually tried it, yet? I would think that native mode would use all 800x600 for 4:3, given that's "native" to the projector. I could be wrong, you'd just have to try it to really tell. I use my computer for watching tv, so it upconverts the 525 horizontal lines for ntsc to 720 for my output.
I think I see what you're getting at, though. Since I have my htpc set for at 16:9 resolution, I have to use the 16:9 mode, or it's vertically stretched. On the other hand, when I run 800x453 (technut) I set the projector in 4:3 or native mode, even though it's a 16:9 feed the projector sees it as 800x600. I think the determining factor is going to be whether the projector interprets your feed as 16:9 or 4:3. I could be wrong, though. This is a little confusing.
JJ