Welcome! The new dynamic of their marriage hasn't really been settled yet, so we're all a little confused. Lois will be accused of an affair with Superman in the upcoming Lois Lane book based off of a photo of that kiss, and the conversation where they were discussing Jon and Lois going into space with Jor El was overheard so presumably that will come out as well. So there's definitely some uncertainty to everything. But Lois and Clark are still "100% together and 100% in love" per Bendis and he's said they won't be breaking up "on any level." The stepfather element is one theory on how this could be resolved within that type of context. But nothing is confirmed. Lois has also told her father that Clark is Superman essentially.
How this all shakes out is likely going to be the next big arc of his run after this first year stories are wrapped up and Event Leviathan as he's promised another status quo shift in how the family deals with each other and presents itself.