I added deterministicLockstep to the Engine using @Evgeni_Popov’s way of recreating Engine in the Playground: https://playground.babylonjs.com/#89YSX9#2
This seems to mostly solve the issue.
It’s still possible to have spheres glitch into each other by rapidly clicking the middle of any pole, but I think this is a separate issue that can be solved by not spawning bodies inside/overlapping one another.