Is it bad that the more spent on the audit and the larger the company the less I trust the results?

I can't speak to your specific case, but I've seen a tool "pass" a billion-dollar company's auditing because the scanner they used never got past the login screen and their folks never noticed that fact.

I'm super glad to hear that happened, but please understand where I'm coming from when I said what I did; reinventing the wheel (as I'm sure you had to here) is straight up dangerous.