I think I have found a solution.
The default tracking pixel is actually the OpenFormula option that is included at the bottom.
First I tried manually including this at the top, but this wasn't successful as the parameter UrlId wasn't being filled in.
After some investigation I came across the definition of UrlId. It's the Primary Key used in table nms:trackingUrl.
Value 1 stands for the value "open".
So I've created a duplicate of the original openFormula but with the UrlId hardcoded on 1. Placing this at the top of the email fixes the issue when the tracking pixel at the bottom isn't loaded.
Also tested the use case where the top and bottom tracking pixel are tracked, expecting this would result in 2 opens being tracked.
But the results showed only 1 open is tracked in this case.