In the end I settled for making my own colour scale - it's a bit time consuming but at least now I can use the count of cell values without the need for helper cells.
For reference, knowing the maximum count would be around 10, I made a new rule for each value (B1:K31 contain the cells I wanted to use the conditional formatting on) like so:
=COUNTIF($B$1:$K$31,B1)=1 - Applies to =$B$1:$K$31
=COUNTIF($B$1:$K$31,B1)=2 - Applies to =$B$1:$K$31
=COUNTIF($B$1:$K$31,B1)=3 - Applies to =$B$1:$K$31
=COUNTIF($B$1:$K$31,B1)=4 - Applies to =$B$1:$K$31
=COUNTIF($B$1:$K$31,B1)=5 - Applies to =$B$1:$K$31
=COUNTIF($B$1:$K$31,B1)=6 - Applies to =$B$1:$K$31
=COUNTIF($B$1:$K$31,B1)=7 - Applies to =$B$1:$K$31
=COUNTIF($B$1:$K$31,B1)=8 - Applies to =$B$1:$K$31
=COUNTIF($B$1:$K$31,B1)=9 - Applies to =$B$1:$K$31
=COUNTIF($B$1:$K$31,B1)=10 - Applies to =$B$1:$K$31
I then used a website to generate the RGB values for a colour scale and applied the corresponding gradient colour to each rule (
RGB Color Gradient Maker).