Yes. You are absolutely right. We cannot know our past perfectly right. We have to guess sometimes. But a good scientific theory will find more and more evidences over time or will be falsified and gets lost after this. That is a big difference to just believing in a story.
Even if I would be only a simple believer and I had to choose - then I would decide for the more likely and more logical story. And even if there are only a few stones as a proof then this is from my point of view much more likely than only a story written in a book a few hundret years ago with no proof at all.
And if we are all wrong and there is something else then I am sure it will not be a god like you describe the designer. It would be beyond our comprehension in a different dimension that we cannot see and cannot understand. In such a case it is simply waste of time to talk about such a creator since he is different and our little stories written in a bible or any other document from other religions cannot describe him. He is supernatural and beyond our understanding.
With that in mind all our relegious stories would be even more unlikely.