It is possible to automate with an automation script but I'm not a big fan of automating it given the financial impacts. For example, if I make a mistake in the physical count that I typed, and the reconciliation is automated, we may end up purchasing more of an item that we already have sufficient quantity on hand to cover. If these are fast moving items that might not be that significant but if these are expensive parts that you use infrequently, that could be a problem. A good reconciliation process gives the reviewer a chance to ask for a recount before reconciling.
Our default out of the box experience didn't really provide a good way to analyze those discrepancies so I could understand why people wanted it automated if they aren't reviewing them today. But a lot of customers aren't aware of what we added in the Manage Inventory work center. This reconciliation process is really helpful to see in bulk what needs to be reconciled and what the impact of the reconciliation will be for you to accept.
In MAS (and Maximo Mobile if you're on 7.6.1.3) we added count books (formerly a Transportation feature) and a new application for executing counts. When you use a count book you can define the criteria for performing the count, see which counts were mismatched, and perform reconciliation at that grouping of records. Customers can still execute ad-hoc counts as well.