They did - Customise > Custom UI and Defaults Switcher. Click one of the options (left) then read in the middle column what's different.
The 2 non-design ones default to ByObject, the 2 Design ones default to ByLayer. Max 2009 Design as installed defaults to one of the 2 Design options (logically enough), therefore it's on by default. Turning it off (ie back to ByObject) should work as you described.
Max 2016 (SP1/EXT1)
Win7Pro x64 (SP1). i5-3570K @ 4.4GHz, 8Gb Ram, DX11.
nVidia GTX760 (2GB) (Driver 430.86).