Instuments with serious intonation problems that are caused by faults in the bore profile, could better be hanged on the wall..
That being said, some things still can be done. Serious intonation errors are almost always caused by an erroneous profile of the neck. Unfortuanately this kind of error occurs more and more frequently, especially in modern sopranos and altos. Another neck can improve (or deteriorate) intonation. When a neck succeeds to exert a beneficial influence on the pitch of a tone (and its partials), the instrument will be better in tune and sound more resonant as well. Necks that are made for Selmer fit Yanagisawa and Yamaha and the other way around. In fact, the designs of most modern saxophones are so much identical, that necks without any problem can be exchanged in search for a good combination.
I made more than a couple of necks for my own instruments to investigate their working mechanisms. Also, in more than one occasion I improved necks for other musicians with diffrent kinds of inserts. In this way we can easily tune a neck so as to reduce any unwished-for sharpness in the second register.
Next, baritones frequently have some intonation problems that are caused by their upper bow. This kind of problem often occurs in older yet otherwise fine instruments. Improvement for the problematical notes, notably E2 and F2 (which in these cases tend to be too sharp) is also found in a correction of the bore profile. An example can be found in the presentation of the «the Martin Baritone» under 'some examples', but I've executed this kind of operation more than once.
If you encouter this kind of troubles, please contact me and we can see what we can do...