As suspected Steinberg have know about this problem for approx 10 years. They pretend they don’t know about it hoping you will go through support and be worn down with endless attempts at a workaround. But basically there isn’t one. The company needs to warn potential purchasers that if they want to record accurate midi, the may not be able to with their software !
System Timestamp not helping with early MIDI notes - Cubase - Steinberg Forums