The way these toxicology reports work is that they test for specific things. It's possible that they didn't test for his bi-polar meds because they wouldn't impact the ultimate report. It's also possible they tested for them and didn't find anything. It's also possible they tested for them, found them in his system, but they didn't contribute. There is no magic test for everything.
As far as Scott goes, I am beginning to think he only ever had two significant stints where he was clean--No. 4-era and Contraband-era. Otherwise, it was either a short stint, he kept drinking, or he was keeping his use under control.
I saw Scott during the No. 4 tour and he was amazing. He was still great during the SLDD tours, but from what I understand he was already dabbling by the time that album came out, maybe even while it was being recorded. For the 2008 reunion, when I saw them on Kimmel after the Houdini Mansion performance, I knew Scott wasn't 'sober.' And while he may have had stretches, nothing lasted significantly.
If I had to guess, I think it was the death of his brother that was the beginning of the end. I mean, less than a year later he was arrested for a DUI under the influence of drugs. A year later he was looking at a quick rehab stint, then he left/was fired from VR, and less than a week later was doing the Houdini show with STP. Nothing ever stuck significantly.
And as I mentioned before, the common denominator between those two sober eras is time off. He went to jail in August 1999, and the STP tour didn't start til May 2000. Sure there was radio appearances and the acoustic tour, but nothing like a normal tour. Scott was arrested in May 2003, he approached Duff about martial arts, and it was a year before the Contraband tour started.
Contrast that with a short February '08 rehab stint, playing your last show with VR, then doing STP a week later and there was never similar downtime again where his sobriety was being cared for.