I have tried running it on it's own and I cannot rotate the screen! So my thoughts were if I ran retropie 4.6 in the raspbian on noobs card it would sort this issue for me as screen rotate is simply on the menu.
I highly doubt that would be possible, just because you start the OS from Noobs. The PI4 model doesn't support 90/270 screen rotation as previous models did, see https://www.raspberrypi.org/documentation/configuration/config-txt/video.md.