This is not a big issue at all. When submitting Krakatoa partitions to deadline the button >Limit To Number of CPUs actually affects the “Limit Tasks To Slave’s Task Limit” in deadline. It wasn’t obvious to me that this was how to turn off “Limit Tasks To Slave’s Task Limit” when submitting partitions from Krakatoa.
Krakatoa build 2.1.5.48953
max 2012
Deadline 5.2.0.47700
Thanks!
The name changed relatively recently in Deadline - originally, it was doing exactly that. Then Deadline added an option to define the Task Limit (it still defaults to the number of CPUs, but could be different), and the name changed, but we forgot to change the Krakatoa GUI. I am off to rename it for 2.1.7 
EDIT: Done, and added tooltips to explain what each option does.