Hi Logan,
I think it is fine to use prescan normalisation, provided Siemens calibrates the receive field once and then keeps it static for the duration of the fMRI scan. As I understand it, this is the case and the acquired 4-D fMRI data is simply divided (voxel-wise) by the 3-D receive field.
Technically, dividing by a non-constant image breaks the MP-PCA assumption of a constant noise level. (You are right that it would not affect S/N, but it does affect N.) However, because of the coil profiles the noise level is already not constant throughout the brain, which is why MP-PCA denoising operates in local patches around each voxel where it is approximated as such. Therefore, if the prescan normalisation image is sufficiently smooth (relative to the patch size), it is not violating this underlying assumption more than it already was.
It is reassuring that you have compared both and that the denoised data comes out nearly identical. The noise level maps should be related multiplicatively by the receive field, i.e., the ratio between both noise maps should correspond to the the prescan normalisation factor.
I hope this helps,
Daan