Hospitals base their charges on resource utilization, not on coding principles, and are allowed to develop their own internal guidelines for how to go about this. There is no coding guideline or regulation that states that a facility can only charge a flat fee for the use of the OR and not also charge based on time.
The facilities where I've coded will either charge based on time, or will charge a flat fee for the initial 30 or 60 minute time period and then charge per minute for any time that exceeds the base amount. There may be exceptions to this, for example, for certain procedures such as an ESWL, which may be charged at a flat fee the whole procedure which is not based on time because of the high cost of the equipment for that type of procedure. But this may vary from one hospital to another. Ultimately, most payers reimburse surgeries at case rates calculated based on hospital costs and acuity, so the differences in charges usually make little difference in the final outcome of how the claims are paid.