I have done exactly that myself because for some reason I couldn't get retropie to run on top the Lite OS. Long story short, I like it. You can set boot order to run Retropie first and you got a desktop environment as a bonus when you exit RP. I have yet to find any disadvantages to that... Space efficiency maybe, if you have a smaller SD card?

@dankcushions It finished while I was at work. Any other updates I should do?!?!
I will remember for next time though... Binary, not source...

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.