I still don't think any of what we saw on screen is supposed to be taken as "fantasy" or Veronica imagining, even the scenes with Veronica in them. What we saw is what happened, in all cases. If "naval intelligence officer" in the way they presented it isn't a real job, that's because this is a tv show (and the writers didn't do enough research). In the world of the show, that's what Logan was (though obviously we didn't get many details of what that entails, so that part is up to interpretation or trying to read between the lines).
And I also still don't agree that we're supposed to think that was the only sex she liked. The reunion scene, which was the only other glimpse we saw into their sex life, was presented as nothing but positive and enjoyable for both. To me the point was more about them being on different pages emotionally (in terms of personal growth, Veronica not accepting/understanding Logan's efforts on that front or seeing any need for herself to grow, etc.), not meant to be taken as representative of their sex life in general. They just used that one particular time (and specifically Logan losing control as the lead in) as an extension or symbol of that. But since really there was very little in the show about their sex life at all, I guess everyone is going to stick to their own interpretations of those minimal scenes we saw, without the presence of additional evidence to go on. For me, though, taken as a whole, I definitely didn't get that they had problems in the bedroom. Their issues were a host of things outside of that.