The most obvious use of magnification is for rendering the entire content larger. For text-based (or more generally, font-based) applications, this means that Assistive Technology (AT) software should be able to request rendering with larger sized fonts or a certain amount of magnification relative to some baseline magnification. Applications beyond standard text-based ones include math, music, and labeled plots/graphics. For non text-based applications such as graphics and chemical structures, magnification could be based on a certain percentage of the normal size or given by “fill this area”. I believe these two ideas can always be mapped onto each other. In all of these cases, the magnification may be due to having the entire documented magnified or it may be due to a request to magnify an individual instance (such as an equation).
There are two other uses for magnification:
used for doubly nested scripts. It is potentially useful to allow the AT to control the maximum percent shrinkage used by renderers. Another possibility is to have a feature that says “don't shrink at all”. Although the rendering would not be consider high quality typesetting, it does make scripts more readable to those with some vision impairment.