I feel it is important to state my credentials before answering this question to establish credibility.
We develop aviation safety software which includes an auditing suite. The audit suite contains IATA's IOSA and ISAGO auditing checklists that airlines use as pre-audit checklists.
Secondly, we work with both IATA certified operators and airlines that have not joined.
Disclaimer: just because an operator has an IATA certification does not mean it is safer. Many airlines game the system. For example, an IOSA-certified Pakistan airline is great at passing an IOSA audit, but the line-level employees know nothing about the safety program. How do I know? I have frank discussions with safety managers around the world about their experiences, and they share some troubling stories.
Regardless of whether an airline is earnest in complying with IATA safety requirements, there are benefits even to operators who are gaming the system.
Now, to answer your question on the value of the IATA audit. Let's consider a scenario where ABC airline wants to do business with a customer in another country, such as flying cargo or conducting operations under the banner of the customer's company.
The customer naturally wants to be assured that ABC airline has a bona-fide safety program. There are two ways to do this. The customer can send auditors to ABC Airline and audit their SMS (safety management system), or the customer can rely upon IATA's endorsement.
Obviously it is cheaper for the customer to rely upon IATA's endorsement.
Also, the benefit is that the contract can close considerably quicker, as the customer does not have to send auditors to ABC airline and spend a week inspecting ABC's operations.
Now let's consider the ISAGO ground handling audit. This requires some background from ICAO's Document 9859 in 220.127.116.11, which I'll paraphrase: "Service providers are responsible for the safety performance of external organizations who are providing products or services supporting the operator's activities, even if the external organization is not required to have a formal SMS."
As you can imagine, airlines fly to different countries where they may need to contract out their ground handling services (fueling, baggage handling, catering). It is easier for the contracting airline to rely upon IATA's certification instead of going to each ground handler in the foreign country and auditing the ground handler every six months or a year, depending on the audit schedule.