Well, the difference between Auto and Standard is that with one you need to use the clutch pedal and with the other you do not (or not -- see the Civic shifting thread
Seriously, you're right, that's an odd set of choices. I assume that "Manual" allows you to tweak the various options by hand (vs choosing one of the percentages, which will tweak the appropriate values proportionately).
Given that a lot of modern chips can overclock themselves dynamically (boosting busy cores while sleeping unbusy ones), I wonder if Auto just means that is allowed/enabled, whereas Standard may tell the CPU not to run above its nominal clockspeed?
What motherboard is this?