Right gave 3.1 a go. This is from a clean install in WinUAE, so very vanilla.
The boot screen looks good and not changes to the 3.1.4 install.
Workbench also looks good and the offset is exactly the same.
Deluxe Paint in 640 x 480 matches the 3.1.4 install
Interestingly, the full overscan screen format does change the screen somewhat. We now have more screen space on the right. The offset is slightly different.
Lastly, we have Imagine, which is completely different. It now snaps to the same offset as the rest of the apps and workbench.
So definitely changed things, not dramatically, but it did change. Next test, I will do this on my real Amiga. BRB.