Fewer calibers reduces flexibility because you have more fixed requirements for specific components. If, for example, you decided to consolidate to 9mm only for handgun loading, or .224 bullets (.223/5.56, .222, .22-250, etc.) there were several months where you would have had little to no market availability of bullets that you could shoot. If, instead, you had also continued to shoot and use, say, 6.5mm in rifles and .40/10mm in handguns, bullets remained available. So you could keep loading and shooting.
Having guns that can use different inputs means that you are not at the mercy of one category of input. Pretty straightforward.