In order to understand the wording of this note, you need to understand how SIF's for tees were developed. This was done using a fatigue testing machine, and real hardware. So, it was convenient for the fatigue tests of tees to be based on the nominal dimensions of the pipe attached to them.
You also have to understand that there is no dimensional standard for tees other than the requirements on overall dimensions and the requirement that the end connections be sized to allow welding to standard pipe sizes. Each vendor is free to use wall thicknesses, crotch radii, and other nonessential dimensions of their own choosing. And they all do. There are burst pressure requirements, and other such things, but they can be, and are, met with many different combinations of internal dimensions.
If you choose to, for example, use a Schedule 80 tee in a Schedule 40 piping system, you probably should use SIF's assuming that the "matching pipe" is Schedule 80 rather than Schedule 40. Richard's note is probably correct from the viewpoint of the internal workings of CAESAR II. The good news is that, if you just accept the values for the Schedule 40 "matching pipe" that CAESAR II will assume, you will calculate a lower number of acceptable fatigue cycles for the schedule 80 tee than you would for doing the calculation rigorously.
And, as Richard's replay states, there is an easy workaround for this if you want to be mathematically rogorous.
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CraigB