Short answer
Compare cost per pallet position only after both designs can handle the same working day. How many pallets arrive per hour? How many must be in the correct load sequence before cut-off? And what happens when a pallet cannot move through the automation?
Start at the dock, not the rack
An automated warehouse can look cheap per pallet position. That price says nothing about two trucks arriving together, an outbound order with a fixed load sequence, or a part pallet that still needs release.
Start with the dock plan and work backwards. How many pallets must the operation receive, store, retrieve, stage, and load in the hours that actually matter?
A cheap pallet position is expensive when pallets do not reach the dock at the right time.
Test the working day, not the brochure
A capacity figure on a brochure belongs to a particular order profile, pallet mix, and staffing level. Change one of those, and the constraint can suddenly sit at receiving, replenishment, staging, or outbound.
Compare both designs on a normal day, a peak day, and a day with exceptions. Not only on the fastest cycle the supplier can demonstrate.
Preventive maintenance is part of capacity
Preventive maintenance is not a line beside the business case. Cleaning, inspections, wear parts, spare parts, and safe access determine when the automation is available for production.
Do not look only at what happens after a failure. Look at the maintenance window, who does the work, and what happens to the inbound and outbound plan when that window is missed.
Is the operation behaving differently from the plan?
I look at the actual flow: process, system, decision-making, and people. That is usually where the next move is.