I'd argue that the religious split and wars resulting were what ultimately enabled Prussia to emerge as dominant and to ultimately split Austria off from the Germanies. Thus, Protestantism was certainly one of the things that helped prevent a German unification on the lines of the HRE's maximum borders.
If you go by the Grossdeutschland definition of German unification, then you’re absolutely right. But if we want to continue the Kulturkampf analogue, we should remember that Prussia did absorb some very strong Catholic states on its path towards welding Germany together. As such, I think an alternative Risorgimento would include significant Catholic parts. But all of this depends, of course, on a huge amount of unknown variables. How come Northern Italy is Protestant? What’s the extent of this Northern Italy? How does it relate to ATL’s definition of nationalism?
Besides, is religion necessarily the main cause? Scandinavia is often presented as the region where national unification failed, but the three Scandinavian states all share closely connected cultures, including the Lutheran confession. This of course came about on account of different developments, within the region as well as in Europe as a whole.