So you want to connect either 3.3V sensors OR 5V sensors to the (one) RJ11 connector? In that case, for 3.3V sensor, I suppose you also want to provide 3.3V power instead of 5V power?
My solution would be to leave the level shifter in place, and (only) jumper the power at the RJ11 side between 3.3V and 5V.
You could use the target MCU's VCC as a voltage source for the data lines. In this approach the CH340 uses mosfets to push/pull the target mcu's VCC and feed it back to the MCU. The same thing applies for signals sent from the MCU to the CH340: the MCU's signal connects the CH340's supply voltage to the input pin via mosfets.