Bore perturbations are generally found in all wind instruments. All of those perturbations have an influence on the behaviour of an instrument. Some of them are common to all saxophones; others you'll meet with only now and then.
In the original patent of the saxophone a 'parabolic cone' bore profile was claimed. It remains to be seen whether we can call the parabolic cone a perturbation. In a historical perspective we certainly can't, simply because it came first. This peculiar type of cone laid the foundation for a number of deviations that are still quite common, but in its pure form it has itself long since passed out of use. The parabolic cone was replaced by a more straight one.
A separate item in the history–section is devoted to these issues. Whoever wants to know more, better clicks to those pages. Incidentally, Sax himself in his second patent of 1866 anticipated the disappearance of the parabolic cone bore.
Other deviations of the perfect cone are more common than exceptional, particularly in bows. Bows, and most certainly the short and wide type of bow that you find as a top bow in the baritone and as a bottom bow in any curved saxophone, behave as an apparent shortening and widening of the bore. For correct register tuning, such effects need to be counterbalanced. Especially the top bow in a baritone, which is active in both registers, needs to be compensated for this effect in a correct way in order to achieve correct tuning. It is true that the bottom bow behaves in the same fashion, but this bow is used only in one register and as such hardly has any influence on the tuning of the registers among one another. Yet, in the bottom bow too, and particularly in many an american saxophone, you often see a clear deviation from the cone (in the form of an S–shaped twist; narrowing at first, then widening).
The cylindrical (!) neck sleeve, which fits neck and body of the instrument together, is a disruption of the cone as well. Depending on the build of the instrument this disturbance is compensated for in different ways: either the neck sleeve is placed in the profile in such a way that on both sides it has a wrong diameter (rescpectively too wide and too narrow). The other way is to place the neck sleeve in such a way that it has a wrong diameter on the instrument–side only (viz. too small). The neck then compensates for this and is too wide directly above the sleeve. This type of build you don't see anymore in modern instruments, French, Japanese or otherwise.
For the rest it remains odd that neck sleeves are (almost) never made with the correct conicity on the inside. This requires no compensation whatsoever and in practice proves to work impeccably.
Bore diameter variations outside this kind of compensations have an influence on intonation as well, but mirrorwise for both registers: a sharpening in pitch in the one register often goes hand in hand with a flattening in the other. The necks of the soprano, alto and tenor saxophone have such a length that they harbour an entire octave of nodes and antinodes and therefore their profile exerts great influence on the correct tuning of both registers in relation to one another (with the baritone, a similar length comprises the crook as well). To reduce the rise in pitch in the upper half of the second register, you find a narrowing in the (upper part of the) neck. The area influences (roughly) the written notes A2 upto and including F#3. Very recognizable is this narrowing in the sopranos of Selmer (mark 6 type) or Yanagisawa, where is has a clearly visible edge. However, in the flowing forms of a curved neck of an alto or tenor this narrowing remains invisible to the naked eye.
The precise form of this narrowing testifies to the importance of the neck in tuning both registers in good relation to one onther, but also in its importance for sonority. After all, when a neck succeeds by means of a correct diameter development to exert an 'ideal' influence on the pitch of a tone and its partials, they will better belong together and the ensemble will sound better. Both instruments and necks are build within certain tolerances and this can still lead to some differences between nominally identical instruments: a neck can spoil or enhance just intonation to a remarkable degree.
Another type of perturbations that inevitably is common to all woodwinds are those regularly spaced bulges of closed tone holes. Although in a saxophone they are fairly small (tone hole chimneys in a saxophone are relatively low), they are not negligible. It is as if the bore is widened a little bit and the effect, by and large, because of a reduced elasticity of the air colomn, is a flattening of pitch. Higher partials especially are influenced by these closed tone holes and go slightly out of tune, the result being that they are no longer harmonics. Next they influence the fundamental they belong to and give it a shift in pitch as well. It all seems a little bit theoretical, but I have chanced upon a couple of striking examples of such influences by partials on their fundamental, even though not caused by the closed row of tone holes. As a rule they are persistent deviations in pitch which are hard to understand and even harder to amend.
Reversely, it means that when an instrument is well tuned, it is also well tuned because of the 'empty' spaces under the keypads. Filling these spaces with a special pads can bring along intonation problems. In the same sense the French acoustician Ernest Ferron states that it is possible to fine tune instruments by trimming the empty spaces under the keypads to a just size.
It will be clear that bore perturbations in general exert an influence rather on groups of notes and not on any one single note. Dents do the same. As a rule, the higher dents sit in an instrument, the worse they are, because this enhances influence on both registers and on partials.