Using a serial port for programming uses it in an unconventional way. The handshake lines are rapidly changed during programming. Normal use of the serial ports has infrequent or no change of the handshake lines. Each change of the handshake lines requires a USB transaction to occur. This same transaction could carry tens or hundreds of bytes of serial data. Every USB transaction takes some time to occur. This is a small amount of time, but will occur many times for each byte of data programmed and makes programming much slower than a serial port on the motherboard.
The FTDI cable you have for the BBB can't be used for programming because it doesn't have a DTR line. It has only 4 of the usual 9 lines and not enough of them are outputs (3 are needed for MOSI, CLK, and RESET).
Faster programming using the serial port can be done with a bootloader that uses the serial port in a conventional way. This is what the Arduino does.
The MiniPOV3 can be loaded with firmware that uses the serial port in a conventional way to update the POV image. This makes updates faster and also eliminates the need to recompile the code.viewtopic.php?f=11&t=4941