hmm, its possible the stm32loader script in the boot loader repo is out of date. Not sure whats happening there.
I wonder why the Arduino-as-serial-passthrough was not working. At the end of the day, the rx/tx lines on an arduino are just hard wired to the onboard FTDI chip. Serial1 on Maple is 5V compatible so no problem there. Its possible that while the rx line on maple is 5v compatible, the ftdi chip on the Arduino running at 5V is not sensitive to Maple's 3.3V output on tx.
Also, as mike pointed out, Vin is a pre-regulator input. Since there is a drop from the regulator, you need to give it something more than 3.3. The official range is 5V-12V, but in practice 4.2V should get you there.
Sometimes, and this is a little dangerous, you might want to have multiple systems running on exactly the same power source. In this case you can provide 3.3V directly onto Maple's Vcc pins. This is handy when comm busses are very sensitive to differences in voltages. However, if you put too much voltage on Vcc directly you can fry the MCU. Its quite sensitive, and will usually smokes around 4.2.