I'm helping to make a new diagnostic for Lyme, which is one of these diseases where patients are often very informed, and traditional techniques fail.
Lyme has many "non standard" diagnostic options. If you run a clean lab, you can sell a non-FDA cleared test directly to a patient without really explaining what it is or allowing anyone "under the hood.". However, to get a treatment prescription most doctors require test results they understand, or at least results from a test that has the backing of a large medical oversight organization (CDC, FDA, AMA...). This is a matter of medical ethics and medical economics. The doctor needs to understand why a prescription is necessary and his insurance need to be able to cover that decision if something goes wrong.
When you have a proliferation of tests without oversight, two things happen: 1) you do get a lot of fraudulent tests, and 2) you develop a terrible relationship between patient groups and medical oversight groups. If you want doctors to treat people based on your test results, your test absolutely must go through serious vetting by some "establishment" medical group (i.e. FDA clearance).
On the positive side, developing tests you can sell directly to patients means you can sell the test for less money, at higher volume, for more overall profit and more overall positive patient outcomes. That is a really, really great win-win situation. It is also far easier right now to get investment for development of a direct to patient test than a "traditional" test. The medical community would be wise to use this current funding environment to help drive patient care forward. The difficult part comes in how oversight is done. It's not going to work to put all of the risk on the front-line clinicians.