It's really quite simple, and it's been explained to you before. Smaller loading gauge is the key; this restricts the size of the body and the equivalent spherical diameter of the cars. Support trusses run along the insides of the vehicles; as the cars are narrower (to enable tilting within a smaller loading gauge), the trusses are closer together which limit the height of the windows. Continental Pendolinos have the same number of trusses but they are further apart as the cars are bigger. The width of the windows are controlled by internal struts and need to not splinter when stressed. Continental Pendolinos have windows that are almost exactly the same width, just taller, like Voyager windows.
The world is (surprise surprise) a very different place from when the APT was designed. The 390 tilts further than the 221. All very good reasons for why the windows are small, they didn't just want to **** on everybody's heads.