Thanks to feedback from @DerDominik I was made aware that Anycubic's default acceleration values in their source code are different from the ones they use in their compiled firmwares. Seems like insufficient torque on the Y-axis caused step loss on TMC2208 for that reason.
Co-Authored-By: DerDominik <derdominik@users.noreply.github.com>
David Ramiro