Most "real" rockets are not on the same scale of size and speed as our model rockets. Thus, the Reynolds numbers are incommensurable.If that were true... most real finned rockets would have ring fins.
My theory as to why the simulation shows a lower altitude than your altimeter showed during actual flights is that the actual motor thrust is higher than the thrust used in Open Rocket. If you look at the spec's, motor thrusts can vary by a pretty wide margin.
But, as you say, Estes model rocket engines can and do have disturbingly variable operating characteristics.
You have a choice to make. Either build and test your own model and drive towards reconciling its anomalous performance with accepted wisdom, or write the whole business off as a misidentification of the planet Venus, and double down on what the authority figures tell you to think.