Maybe I don't understand the Throw properly, because I fail to see how the length of shaft is going to change that.
Think about how you can achieve leverage on a rusted bolt, using an extension on a wrench. The bolt is the center of a circle, and the extension is the radius. The further out you hold the extension, the larger the circumference of that circle becomes, and the larger the circumference, the further you must move to achieve the same turn distance at the bolt. When you are dealing with sub-millimeter distances for switch actuation points, long shafts can lead to a sloppy, or unresponsive feel to the stick.
Just like the bolt analogy, longer shafts are also capable of putting more force on the joystick body and/or centering mechanism. This can make a strong return feel very light, or a light return feel like nearly nothing. Desirable to some in some instances, but not so good in others. No particular aspect of a joystick design exists in a vacuum. Durability, feel and responsiveness all rely on those design aspects working together, so always be careful when making changes. In the end, however, if you like it and it doesn't damage the unit, it's all good.