The PAD3V5V pin determines the slew rate for output drive pads to keep the rise time the same for a 3V configuration and 5V configuration. Yes, it is work in both cases, it is not dangerous anyhow to have it set in opposite configuration.
Shadow flash programming may be potentially dangerous because there is also censorship information there. Censorship feature is a way to prevent unauthorized access to the device. However it is very sensitive thing. It is needed to use it very carefully, because an inappropriate usage can lead in making the device useless. If user accidentally erases shadow flash/row there is no chance to recover it (unless it had been though about before).
In other aspects shadow flash is normal flash memory and may be programmed common ways. Example you may find here:
https://community.freescale.com/docs/DOC-102582
I would strongly recommend to read mentioned appnote.