I can't think of a better way to write "the user" in your sentences, only to reword them so you don't need to use it as often. Whoever is reading the sentence understands that "a user" will be using the software and doing the actions, without needing to explicitly say so.
To me, it stands out more that you reference the elements so often, and that you talk about the user "detecting" the boundary instead of the user "seeing" it, or the software "making it visible".
"Highlight" already means "to draw attention to something", so it might be redundant to explain why there is a highlight, depending on how important the element boundaries are.
And the phrasing "the x of the y" is more common in other languages than English; you write "elements of the page, boundary of each element, elements of the page, features of an anchor". It is clear and understandable, but it feels like hard work. "Elements of the page" can become "page elements", and after you have written "elements of the page" once, you don't need to refer to them as "elements of the page" again, instead of just "elements" (unless the context makes it easy to confuse them with other elements).
e.g. I might write:
Page elements are highlighted as the mouse moves over them, and the user specifies anchors by selecting one or more elements. For each anchor, a dialogue allows selecting or defining anchor features by text value, text patterns or attributes (e.g. id, class). (Figure 2).