and you look at this tool with your eye,,i think its been mentioned above that the idea of carb syncing is to balance the actual vacuum between the cylinders not actually get the slides at the same height,which will get the bike running ok then use a vacuum method,leaving them set where the precision instrument aligns them is precisely wrong.
Your eyes and a visual inspection is the first step to any mechanical or welding procedure.
I do understand your concerns about the amount of vacuum being created in each cylinder.
It's a case of using the right tool for the right job. The verniers are the right tool for initial set up but not for fine tuning, for fine tuning you use the vacuum sync to get it just right.