Short answer is, calling a woman obasan is getting uncommon these days unless she is a real aunt, mostly because obasan implies the woman is old (and maybe Japanese soceity is aging fast?).
One factor is that Mizuto is mature enough not to need a mother really. If he is a child, calling Yuni okaa-san/mama just after remarriage may be possible, but the relationship between Mizuto as a teenager and Yuni as step-mother does not look so close yet. This means, Yuni is essentially just a woman much older than himself, whom Mizuto would call with honorific alone (i.e., step-mother-ness does not really play a role in their relationship).
Ojisan has the same issue as obasan, but using ojisan is avoided less. Though ojisan can be used for any male, in this case Mineaki ojisan may soundssound more like they are family.
You could perhaps think this way: to some extent, using Yuni obasan and Mineaki ojisan could have been the default in Japan of dozens of years ago, but due to the increase of age sensitivity on women's side, just oba came to be dropped.