Hi Manuel,
If you really want the FOD images at the same resolution, you could always down sample the T1w image (with mrresize) to be the same resolution as the DWI before using it in the -template option of mrtransform. If you use piping you don’t even have to save this as an intermediate image.
Performing CSD on the higher resolution image will perform as expected. However, I guess it depends on what you plan to do with the FOD images afterwards. I typically work with up sampled data in a fixel-based analysis. However for tractography, changing the resolution will affect the default step size and therefore the output streamlines. For related posts see here and here.
Hope this helps,
Dave