Well, the issue with the code in #1 and #22 is that they don't connect via UART, which is seemingly the only way to reach a full-step resolution with the TMC2209.
Your point about acceleration does make sense to me, though there is an acceleration value in the code in #38 - so maybe I could poke around and try to find an alternative to VACTUAL that would use it!
I will add that research is suggesting to me that a stepper motor of this size and step degree is really not designed to reach 1000 RPM and that I may simply be pushing what the technology is capable of doing right now.