I ride a Canyon Endurace, and like you was a little surprised at their sizing recommendations for an S (my previous bike was a 54). But my understanding is that
I had a professional fit done just after I got it, and the frame sizing was spot on. The fitter recommended swapping the installed 100mm stem for a 90mm, and I had no problems swapping this over with Canyon (including the additional integrated handlebars that I purchased). Canyon policy is to work with you to get the fit right, and will pretty much swap anything (up to and including the whole bike) in the 1st 60 days.
I agree with the suggestions of measuring twice, and getting someone to help you - ensures you are standing straight, the tape measure is positioned correctly, etc.