The Emphasize Negative Numbers setting squares off the edges of the “pill” (or bubble) around any negative number.
As you can see in the image below, this setting affects budget category Available balances as well as negative Account balances, i.e. credit cards and other debt accounts.
A potential value-added scenario for this setting might be if the Colour Blind Mode adjustments didn’t effectively address a user’s visual impairments. Otherwise, meh. But if it does the job for you, go for it.