TR is a more aggressive protocol, with more testing and increases as soon as 3 days (6 cycles). The reduction point is lower and you can increase quicker per protocol because you are testing more, which lets you know how your kitty is responding to a particular dose. Also when following TR protocol, you are feeding a wet food only diet. If you are feeding any dry food, you would need to follow the SLGS protocol. SLGS, while still a good protocol, is more conservative than TR. A person might choose this protocol if they are unable to test as frequently. As a result, the reduction point is higher, doses are held longer, and curves (testing every 2 hours for 12 hours) are done once a week to see how the kitty is doing on that dose. After a curve, the kitty's dose can be increased and then held for another week.
I can't remember the exact whys, but dry food can add variables to the BGs that don't work well with TR protocol, so that's why dry food is only given with SLGS protocol. Free feeding is okay, although just remember to pick up food within 2 hours of preshots to avoid the PS number being food-influenced.