Grocery store A (with JIT) has much less inventory, which has a variety of benefits. It needs fewer square feet, which reduces rent/heating/lighting/cleaning costs and therefore reduces prices; this also means more residential space for actual residents. It has less food waste, because most inventory is only on a shelf for a hours or days rather than weeks. Paradoxically, it is actually easier to keep goods in stock, because there are 10x fewer goods to count.
By contrast, Grocery store B (without JIT) has much more inventory, which has a variety of costs. It needs more square feet, which increases rent/heating/lighting/cleaning costs and therefore increases prices; this also means less residential space for actual residents. It has more food waste, because inventory is sitting there for weeks or months to prevent a shortage. Individual items go out of stock all the time, because the staff can't effectively count this much inventory.
Similar arguments hold for stocks of parts at factories, with the additional problems of obsolescence, things getting lost, risk of fire or shelving collapses etc. Carrying enough inventory to weather a shortage like recent COVID shortages would require months and months of inventory; imagine the obsolescence costs if the factory needs to make any change at all!
We need to stop blaming just-in-time logistics for shortages. Outsourcing, deregulation, anticompetitive behaviors are all valid, but just-in-time logistics makes businesses much more efficient which helps everyone. The thought of having stockpiles large enough to prevent issues like recent ones is completely absurdist.