Do you know what aspect ratio the camera was set to for the DNG you sent?
I just checked the JPG from this shoot. It is 4000*3000 so the ratio must be 4:3.
Ok, just to be 100% sure, can you can take a DNG with the jpeg aspect ratio set to 16:9, and check that the DNG has image in the whole 4:3 frame? I'm 99% sure it will but might as well make that 100%
May be some lines on the Display for 16:9 should be helpful. Is there any option in CHDK to do this?
Do you mean just for framing? CHDK lets you create custom grids. The canon firmware might have a 16:9 grid as well. The script also lets you set the resolution (which usually includes aspect ratio) in the "Image size" setting, so you could compose in 16:9 and have the script to something else. Maybe I misunderstood?
I think your last test shows is expected behavior. Overexp protection only reaches max weight a bit above the "limit" value due to the /120 "slope" factor in calc_ev_change, so the meter being below target partially cancels it out. You could set the limit down to 1%, or increase the Overexp Ev range. I'd suggest the second option, 1/4 stop below over exposure really isn't much.
You could also change the /120 to /100 to make overexposure protection stick closer to the actual limit. I originally put in these factors when histogram precision was limited to 1% increments.