The customization does not change the stat's nor reduce the size category.
A hand axe is normally sized to fit comfortably in a human or a dwarfs hands. A windling can wrap their hands around it, but it would feel the same as a human wrapping their hands around a fence-post. it can be done, but is not really comfortable and it is likely to be held awkwardly.
A windling who found a nice hand-axe that they liked might pay to have a new haft put on it, thinner and shorter, with a different center of balance. More comfortable in the windlings hands and arm, and designed as a two handed windling weapon, not a one handed dwarvish one. So new haft, but the axe head remains the same. A dwarf who picked up that hand axe would find the handle too short and light for his taste.
The text you quoted did not specify any penalty for a windling using dwarf sized weapons or visa versa, so it can probably be done in a pinch without penalty. But it would just feel very wrong and uncomfortable.
Most weapons are available in windling sizes, they just did not bother to list more than a few.
here
http://pandagaminggrove.blogspot.my/201 ... troll.html
somebody unofficially lists additional windling and troll sized weapons.