The programming includes a latch-up protection. This protects your radio in case you connect a powered programming cable while your radio is off. This protection might not be necessary, but it doesn't add much to the cost. In the least, it serves as a demo how to protect devices in cases where it's needed.
Kenwood/Baofeng programming connection
The Kenwood plug has a separate RX and TX-signal. The FTDI cable sends data to the Kenwood using the FTDI_TX signal. On the Kenwood side, this is pulled up to 5V using R2. D5 prevents latchup on the Kenwood RX-pin (B_TT/RX).
When the Kenwood sends data back to the FTDI-chip. It uses the B_TX-signal. When B_TX goes low, the FTDI_RX pin goes low as well. Q1 prevents latchup on the B_TX-signal.
For the Yaesu FT-65, the RX and TX share a common Y_TRX signal. This signal is pulled up internally in the radio. The FTDI can send data to the Yaesu by pulling FTDI_TX low. Diode D1 prevents latchup.
When the radio wants to send back data to the FTDI, it pulls Y_TRX. D1 prevents the FTDI_TX output of the FTDI from being pulled down. When Y_TRX goes low, Q2 assures that FTDI_RX goes low as well. For Q2 to work properly, its gate should be tied to 3V3. Unfortunately, the Yaesu radio doesn't provide a low impedance voltage source output. The Y_TRX is used here to charge C1 to 3V3.
Yaesu audio output
The Yaesu's audio output signal is Y_SPK+ is connected to the speaker in the Kenwood headset through resistor R7.
This audio signal is also sent to the TNC connection. A voltage divider is added here to limit the signal amplitude. R1 and R2 might still need further tuning.
Yaesu audio input
The Kenwood has a dedicated PTT-pin, while the Yaesu shares that pin with the microphone input. When the PTT-button on the Kenwood headset is pushed, B_PTT/RX will be low. Q3 will start to conduct and the Kenwood headset's microphone (about 1Kohm) will be connected to the Y_MIC pin. The Yaesu senses this low impedance on its MIC-input and will switch to transmit mode. R4 is 100Kohm to avoid excessively loading the microphone input of the Yaesu radio.
For the TNC connection, the PC sends audio on its left audio output, which is capacitively coupled to the Yaesu microphone input. To put the radio in transmit mode, the FTDI_/RTS-pin needs to be pulled low.