None of those interactions are main story. The only godly interaction tied to the main plot is basically a short scene of Lumia.
They really haven't been tied to the story other than that, all of their scenes are optional.
If we dismiss optional content as not being important, then the whole bit with Gweyr is not important. Which you really can't do, as her optional side quest pretty much explains why Garth, Garret, and Gwyns family is the way that it is. Just because content is optional doesn't mean it can't have a greater impact on the story or that it has zero merit to be explored. Recruiting most of the people in Mass effect 2 and doing their loyalty mission is all optional. But, it explains your companions motivations and why they are capable of certain things.
Edit: You're only required to recruit Jacob, Miranda, Mordin, Jack, Grunt, and Garrus, but it is possible to skip Tali, Samara, Thane, Kasumi, Zaed, and you can sell Legion to the Illusive Man. Just cause you skip these characters doesn't mean they and their content suddenly doesn't exist. It doesn't mean the events in the story doesn't happen or play a larger role in the story. For example Miranda is infertile. The only way you can know this is if you read the codex in Lair of the Shadow Broker. If you chose or miss that content its on you. As that content can inform on certain things about her personality. Like Miranda questions why Joker wouldn't want to date a human. This might come across as her being weired out by Joker dating robot, but having additional information about makes it possible to infer that shes wondering why someone date someone they can't have kids with as that's something she wants.
Javik is optional in Mass Effect 3, and a lot of people were upset over that because having Javik explains a lot of things about the Asari. How They came to power and the world of Mass Effect as a whole. And many people argued that he should be a required companion as the greater implications that come from interacting with him completely changes how people view the world of Mass Effect.
Edit: Also if you don't agree with Tau_Iota ideas I think thats a reasonable stance to take. But some of your other points I can't really agree with.