Not necessarily, it could just be a very subtle mismatch due to machine precision – see this thread for details.
However, if there is a genuine mismatch, it might be worth chasing down where this mismatch originates, and which of the sform or qform is to be trusted…
If you have it, yes – though that has no influence on the warning you get. It just means that any additional information present in the JSON will also be injected into the header of the mif file. You’ll basically end up with a single mif file that contains all the voxel data, the bvecs/bvals, and any other information present in the JSON. 