If it is a commercial contract that pays at a percent of charges for outpatient services, then the CMS Outpatient PPS methodology shouldn't matter.
That being said, it's important to look at the language of the contractual agreement and any amendments/exhibits/communication that are part of the contract.
If the contract has specific language about implants, then that would override anything that I say below.
Based on my past experience working in managed care contracting departments, a very general summary of percent of charge contracts:
Typically a payer and provider enter into a percent of charges contract to make it easier to administer. For example, it could be a small payer that doesn't have a sophisticated claims processing system. Or a rural provider that doesn't get a lot of volume but the payer needs to keep in network for coverage purposes.
The payer usually isn't going to complicate processing by looking for PPS SI indicators, because ease of administration is usually the reason the parties entered into a percent of charges contract.
They might check for some basic unbundling edits to ensure the provider isn't padding the bill, and they may do some charge audits to ensure that the services charged on the claim actually match the documentation.
But they're not usually going to look at SI indicators
unless the contract documents specifically state that PPS methodology will be used.