The general notion is - why re-invent the wheel?
A variety of modules are available, including ones as cheap as $2 (albeit not the FT232, but the difference is only in the drivers) which are cheaper than sourcing the chip itself. They can be soldered to a main board - or socketed. They can be fitted over other parts making the design more compact in the process.
The only real advantage of a 16U2/ 32U2 is having HID functionality or tandem processing.