The modem in the icon clearly isn’t an acoustic coupler style modem, though.
I think putting the modem under the phone was just a space-saving measure. The modem had to be close to the phone (for cabling reasons), and it was big and flat, to putting the phone on top of it took less space on your desk than putting them side by side.

By the mid-90’s this didn’t work any more since modems were now to small to balance a phone on them.