Odd, then, that SME would bother to state that the alignment protractor is based on that assumption, if the measurement makes no difference.
There is a theoretical issue if you get round to writing a page or two of tonearm math as the way SME arms work is to align by altering the effective length and pivot to spindle distance. It is, like all tone arm math involving a pivoted tonearm, imperfect. A compromise. It does however work very well in practice and a SME tonearm, due to its exceptional ease of use in setup, tends to end up with a very low distortion alignment. This is something for audiophiles to just follow the manual to the letter and forget about unless they are genuinely capable of understanding several pages of complex algebra and think they can second-guess SME.
There is an inherent error in all pivoted tonearms, they are remarkably imperfect things that at best are in correct alignment at two points on the record surface. The important thing IMHO is to use the arm exactly as designed, e.g. set it up with the manufacturer’s protractor and instructions. The problems come when people try to force an arm into alignment with the wrong protractor without understanding offset alignment etc.
The tldr here is just not to overthink it. SME know what they are doing, a 1mm tip to mount lug discrepancy is nothing and the whole arm slide assembly exists for exactly the reason of compensating for this. If it is aligned correctly with the SME protractor it is the best it can possibly be with this arm/cart combo. There is also a little slack in the headshell screw holes, so if being really pedantic (not necessary) then nudge the cart as far forward as it will go in this specific situation. It really isn’t a big deal. I’m prepared to bet most people here, especially those who rely on dealers to fit carts, likely have a larger error. For clarity: the error here will be a micro-fraction of a degree out of offset alignment as the effective length becomes a variable to a small degree. It is insignificant, almost certainly less than the stylus manufacturer’s own positional tolerances. To better it you’d need to get to Fremer’s oligarch-market microscopes etc. Just don’t over-think it!
PS The theoretical error here is almost certainly less than just about every old-school Linn LP12 in existence where the armboard position presents a *huge* variable (several mm) in pivot to spindle distance due to having a lot of slack in the mounting holes to the subchassis unless setup with very, very precise measurement. Which it almost always isn’t.