Allowing liners benefits large calibers over small ones. Disallowing liners, OTHO, benefits small calibers over large ones. All else being equal, I'd rather give the benefit to the big calibers even though I, personally, carry a small caliber. It's also just a good simple system. Either it broke the line, or it didn't. It makes for the easiest, most repeatable judgment. That's why almost every shooting sport uses it as a standard.
Holding folks to tight standards is great. But if I wanted folks to shoot a half inch smaller group, I'd reduce my scoring zone by half an inch.