According to M. Moakher's
Means and averaging in the group of rotations
and I. Sharf's
Arithmetic and geometric solutions for average rigid-body rotation
the distance between two rotation matrices is $$\| R_1 - R_2 \|_{\text{F}}$$ where $\| \cdot \|_{\text{F}}$ denotes the Frobenious norm. Does it mean $\left\| R_1 - R_2 \right\|_{\text{F}}$ or $\left\| R_1^T R_2 \right\|_{\text{F}}$?
$\left\| R_1 - R_2 \right\|_{\text{F}}$ does not make sense as $(R_1-R_2) \notin$ SO(3).
$\left\| R_1^T R_2 \right\|_{\text{F}}$ is also strange: suppose $R_1=R_2$, the distance is $3$. I find out that the distance between two rotation matrices is less than $3$. Such metric is against my intuition (the distance between two identical elements is largest!).
It means $\|(R_1-R_2)\|_F.$
It does not matter that $R_1-R_2$ is not special-orthogonal as we can still take the norm. Consider that the distance between two points on a circle is related to the length of the vector between them, even though that vector is not itself on the circle. This is much like the $SO(2)$ version of your question.