I think you might be confusing space with resolution and field of view. The MNI space can be expressed in any voxel size and field of view. This will mean that shape of the data in voxels will be different. Some tools take this into account and apply interpolation on the fly (fsleyes, Mango, nilearn), but some don’t and throw an error if the shape of the data in voxels is different (fslview). This does not mean that the file you are working with is not in MNI space - it only means that the data is not resliced in the exact shape as the particular atlas you are working with.
Practically speaking you need to reslice your atlas to the resolution of the files produced by FMRIPREP (for example using nilearn’s resample_to_img) or extract timeseries from the data using a tool that does interpolation on the fly (such as http://nilearn.github.io/connectivity/functional_connectomes.html).