on latest available version, only other mods present are rate calculator and alien biomes. from what ive seen on youtube they should be ok.
train with cube in fuel slot gets the bonus, AS EXPECTED (the cube gets locked in tho, so i assume its not the intended way to do things)
train with coal as fuel and cube in cargo wagon slot does not get the speed bonus, NOT EXPECTED. both in manual and auto mode
i can provide the save file or any other info you might request.
PS really really fun mod :)