I’d choose the method based on the accuracy and robustness on your data.
transformconvert can convert flirt or ITK transformations. Unless bbregister uses one of these file format conventions (I don’t know), this conversion to mrtrix format won’t work. You could create an identity warp and warp that to target space using mri_vol2vol to make a (linear) warp file as described in the wiki. Alternatively, you might want to use flirt with the bbr-type cost function.
This might be related to a long dash issue.