There are a large number of variables in any audit assignment. First of all is the auditor. A Big 4 auditor is many times more expensive than a smaller auditor, but for the majority of public companies, a Big 4 auditor is not appropriate. Many smaller auditors have very good reputations and are more than capable of properly auditing a smaller public company.
The cost also depends on the complexity of the company being audited. Those with no revenues are much cheaper than those with revenues, and obviously the larger the amount of revenues the more time it takes to properly audit and thus a higher cost. It also depends on number of customers and location - foreign locations cost a lot more to audit, as an auditor may have to travel to the locations or hire another firm to audit that portion. You also have to factor in Section 404 compliance. Going forward, this is less of an issue due to the provisions of the JOBS ACT exempting EGC's from the auditor attestation requirement, but assuming this company in question has a market cap of shares held by non-affiliates of less than $75 million, they are exempt from the attestation requirement.
As Bar1080 pointed out, real companies maintain accurate records, so that cost should already be excluded from this discussion as it should not matter if they are public (and fully reporting) or not. For fully reporting companies, your costs are the audit (which is just once a year - quarterly results are unaudited) and the SEC reporting.
For the Company you described, $40-$50K per quarter looks to be much too high. Agsin, the cost would vary widely based on the factors above, but total annual costs for being fully reporting for a company with $2.5 million in revenue will probably fall in the $50-100K range. Total.
