rs485 and serial ISP
I can't understand the purpose of connecting *RE/DE to GND/Vcc. With
this setup, the driver inside the transceiver is always enabled, and
it's always driving the A/B pair. Meaning the device at the other end of
the link cannot drive the pair itself without making a collision.
Basically you have a simplex link, where the Pro Mini is always the
sender.

The normal way to connect an RS-485 transceiver is to have DE driven by
a GPIO pin of the MCU. You pull this pin HIGH when you want to talk, and
leave it LOW the rest of the time so you can hear other devices talking.
The *RE pin is connected either to GND (if you want to hear the echo of
what you say) or to DE (if you don't).

That being said, you are correct in that the transceiver may cause
problems when uploading the firmware on the Pro Mini. One possible
solution is to put a resistor between RO and A-RX. The TX of the FTDI
cable should have a low output impedance and be able to overpower that
resistor. Another option is to use ICSP (in-circuit serial programming)
instead of going through the bootloader. It would be easier if you can
put an ICSP header on your board.