Measuring cylinder protrusion
You are correct. The manual specifies measuring the protrusion with the O-ring seals in place, but it also calls out for the retaining tool to be in place and torqued to about 10 ft-lbs. One might guess that this would crush the O-ring sufficiently that the cylinder was metal-to-metal at the bottom.
The assembly procedure appears to assume that one is actually building the engine rather than just checking things prior to a final re-assembly. I would expect a non-O-ring check to be a valid confirmation that the cylinders were at the right tolerance.
Anyway, here's the sequence from the manual.
Carson City, NV
59 102 Touring (first Alfa $500 running)
65 Sprint GT (2nd Alfa, $500 daily driver)
102 Sprint (never did anything with it, but wish I had)
74 Berlina (first new car - now certainly rusted into oblivion)
61 Giulietta Spider G-Prod Race Car (where is it now?)
84 Spider Veloce (rarely drove it, so sold it)
86 Quadrifoglio (Dull car - no more 115s for me)
59 102 Touring Roadster - restoration complete, enough Alfa for any rational man. Or irrational, for that matter
1971 Alfa Montreal (see above comment regarding rationality)
Two 1946 Stampe SV4C (c/n 294 "Rocinante" - wife's favorite airplane. RIP), and c/n 235 "La Bon Temps Femme" (gone to a new home, but never forgotten)
Zlin 50LA (+9 -6 gees, titanium spar, 1200 lbs, 260HP rumored to now be in Brazil)
1946 Luscombe 8A
Starduster Too (recently spotted at the Nevada City, CA airport - over 20 years and an entire continent separating it from our stewardship in Binghamton, NY)
1955 Cessna 170B (wife taught me to fly tailwheel in this)
64 Mooney M20E ("Rambo". My faithful steed for over 30 years) Nearly 50 years old, and just returned from a trip to Argentina in him
Newest in the fleet
1967 Piper Super Cub on Wipline amphibious floats (a true "all terrain vehicle")
2010 Triumph Thunderbird
You can snap roll an Alfa only one time...