I have a 3.5" screen for my pi3:
It can be powered via the GPIO pins, is it safe for me to connect this on top of a brickpi3? I’m not sure what all the brickpi3 does to the outputs on the pins on the top of the board.
You can use the BrickPi3 schematic as reference for which pins are used. If the display doesn’t use any of the GPIOs being used by the BrickPi3, it should be fine to use them together, but I doubt that’s the case. Additionally, depending on the display’s power requirements, you might need to supliment the 5v power supply provided by the BrickPi3. From briefly looking at that display, I think you could run an HDMI cable to the display from the RPi, and source the display’s 5v from an extra power supply. If you don’t stack it on the RPi GPIO pins though, I don’t think the touch input would work.
I think it would be safe, but it likely won’t work to stack it on the GPIO pins.
FYI the screen will not get power via the GPIO pins when placed on top of the brickpi3 but other than that it works just fine. You cannot press it down to be 100% flush with the brickpi3 though, some of the hw on the bottom side of the screen collides with the motor/sensor ports on the brickpi. I power the screen via one of the pi usb ports with one of these short cables
https://www.amazon.com/gp/product/B078K656BR/ref=oh_aui_detailpage_o00_s00?ie=UTF8&psc=1
Thread here on how to get the screen to work on ev3dev