The distances I used are total distances from the Tour stats pages and relate to the two measured holes at each tournament. They are selected on holes where the Tour feels that most players will use drivers. They, of course, can't control what a player chooses to hit.
At last years Valspar Championship, I happened to run into Mark Russell on the course during the final round and since he was unoccupied at the time, I asked him which holes were the driver distance measuring holes. He didn't know but radioed in and found out. They were two long par 5's running in opposite directions. He was curious why I wanted to know and I told him that it was because some of us were debating whether the driving stats were skewed by players hitting less than driver. He just said they tried to pick holes where there was no reason for any of the players to lay up or want to guide their shots. I watched for a while at one of the measured holes and 15 of the 16 players I watched hit driver - the other hit a 3 wood. So, in practice, it seems likely that the driving distances may be slightly understated based on this one anecdotal example. However, this has likely been the case over the life of the measurements.
There are, of course other factors that vary from round to round and course to course including weather, course conditions, etc. The data does not exist to do a year to year comparisons that isolate all those other factors. Since there are thousands of drives included in the data each year gathered in all kinds of weather and course conditions, I'd guess that these factors more or less wash out from year to year.
Bottom line is, that based on the most comprehensive data available, average driving distance on the PGA Tour hasn't increased by much, if any thing at all over the last decade. Whether that current average distance is "good for the game" or not is another debate. At least on the Tour the bleeding has stopped, more or less.
In the spirit of you learn something every day, who knew that TD was a conspiracy theorist?