Most programming is done at 5V. All the ISP programmers operate at 5V. Will there be any issues if the Arduino MCU is programmed at 3.3V through UART?
Once the (matching) bootloader is present, 3.3 V versions such as a 3.3 V Pro Mini (running at 8 MHz) can be loaded though the bootloader at 3.3 V.
Inadvisable at 16 MHz.
If arduino is powered with 3.3V, running 8mhz with proper bootloader, and uart is also 3v3 then there shouldnt be any problem.