Welcome to the world of complications of relationships.
The problems you allude to aren't the only ones.
In addition to steps showing up in descendant charts and reports as if they are descendants of a step-parent (regardless of who is preferred), if you select a step-parent as the preferred parent (over the blood parent) and run an ancestral report, the report will be ancestors of the step-parent - who aren't related to the step-child.
I suggest people never enter any parents except natural blood parents and never setup step relationships. Make all your reports one of blood begatting blood. Otherwise, you will end up in a bloody mess after a few years.
You are dealing here with your own family and people you know. As the years go by and you enter more and more ancestors and prior and subsequent marriages of spouses, you will end up with mistakes that you don't even recognize becaue you forgot that Jim Smith's (born 1850) 4 generations of descendants should not be in his step-fathers list of descendants.
As for the relationships show in the upper right of the family tab, or in the Relationship Calculator - I would suggest to make suggestions to their enhancement page. This relationship calculator is pretty good, but it still comes up with questionable relationships.