Inconsistency can indeed present at least the appearance of discrimination, when people of different races, genders, etc. are treated differently--and a sufficiently strong appearance can result in liability for employment discrimination even if there was no actual discriminatory effect. It is advised to standardize on policies like how to request leave, documentation to provide if requesting an accommodation, etc. You can preserve the flexibility to change policies and act with discretion by stating prominently in the handbook (and having the employees sign and return a sheet saying) that "All employment is employment at will, and nothing in the handbook creates a guaranty or contract of employment. This handbook is informational only, and policies therein are subject to change." That way, you have a guide to ensure consistency, but are not locked in to it as if by a contract.