"Close perfectly"?
Do you mean simultaneous pad contact with the tone holes, or equal closing pressure? Because of metal flex, and somewhat because of the similar 'give' in linkage silencing materials, the two are mutually exclusive. Mechanics 101.
And these discrepancies cannot be "tweaked out", unless by deliberate design, design, the flex is the same along the path from the finger to each pad involved in a linkage. Also mechanics 101. No manufacturer has achieved that yet. The situation could be helped a little if the pad at the end of the route with the most flex, was firmer than the pad at the end of the route with the least flex. IMO this is the only way that flex could be compensated for.
It's all a matter of best compromise, which is often quite precarious. Whether a player is into jazz, or orchestral, or a beginner, the adjustment is all the same to me - the best it can be for that particular design of sax. The more servicing I do, the more that I realise that as with ALL mechanical engineering, everything is a managed compromise; nothing is 'perfect', thanks to the 'give' in all materials.
Actually I think the purpose for the B activating the C# is for a cleaner change BETWEEN these notes, rather than so that B can be leak-proofly played with the C# key down as well. On a well designed 'touch-piece' geometry there is no need to press down both these keys at once while a note is sustained.