Well that's a different question.
For 423.2.3 I would use t nom - your CA.
Whilst the t for your design was only 2.8mm, you have quite rightly chosen a pipe much thicker than that for practical reasons and IMHO, you can use that additional metal in the relevant calculations. this is because it specifically states ..to be operated...", hence the actual reality of life in that you have a much thicker pipe than you need comes into play.
How autopipe works isn't that clear to me, but maybe if you actually insert a CA it will (or should) use t nom - the CA. Therefore it is not conservative, but actually following the general principles of the code to remove the CA from the nominal.
I don't understand your comment "...2.8mm (which includes a 12.5% mill tolerance)." B 31.4 or 31.8 do not include manufacturing tolerance in their calculations of t. This is stated as being "allowed for" within the design factor used in the calculation.
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