When comparing tubing with the same ID and length, we see a significant difference in output between PTFE and silicone tubing.  Question is....is it because of a chemical reaction or internal surface smoothness or other?

The most logical guess is chemical reaction.  We know, all-be-it a visibly small amount, silicone degrades in the presence of ozone.  When does it begin?  If it degrades (chemical reaction), it begins with the first contact and not when one sees yellowing or observes more brittle tubing. 

In the YouTube "tubing makes a difference" we compared apples to apples meaning same ID, same length and all testing conditions the same.  It is important to note that an unnecessarily large diameter tubing results in degradation of ozone and wastes time in the process at common flow rates of 1/32 to ¼ lpm,   The larger the ID, the slower the flow and delivery...significantly slower, as shown in the video.  Not only does it waste time, but also allows more time to degrade, and more time to be in contact with the tubing material.  If a chemical reaction is occurring with silicone, or other material than PTFE, a larger diameter will increase contact time, magnifying the degradation process.

When one sees 3 or 4 mm ID silicone tubing being delivered with a "kit", the tendency is to utilize it regardless of size and length.  This “Tubing Makes a Difference” video shows the negative impact of larger ID and longer tubing. In contrast, comparing larger diameter or different lengths of PTFE, the degradation is minimal.

The real question is not what happens... but why not simply use PTFE?  Considering 1/32 to 1/4 lpm flow rates, all one needs is 1mm ID PTFE.  It is strong, flexible, not chemically reactive and durable…lasting indefinitely    Excess length of PTFE has minimal impact on concentration.   Another important consideration is time spent waiting for ozone to be delivered.  As the video shows, at 1/32 lpm, using 1mm ID PTFE tubing, delivery is within seconds, compared to silicone 3-4 mm tubing exceeding minute or more.  PTFE provides a higher concentration in a fraction of the time resulting in a more efficient treatment protocol.

For your consideration see "Tubing makes a difference"  https://youtu.be/1MQa8RnGf4k

Note, the data was collected "real time" and did not record the actual peaks or lows but was close.  For the graphs, we went back, and with stop action were able to establish points with more accuracy. 

Look at the difference comparing 1 mm ID Silicone to 4mm ID Silicone.  Note, 1mm ID silicone is not practical.  However, it was used here to show the impact of diameter in both peak delivery as well as the time to reach that peak.