They don't sync well in Logos 4.
1) If a Biblical verse is only cited in a footnote, the correct footnote is not highlighted when the visual filter is on. This is in contrast to Logos 3. As a result, I have to hover my mouse over all the footnote references and read them to find my verse. Try, e.g. Hos 1:9 in the "ל" section of Waltke's Introduction in Logos 3 and Logos 4.
2) I usually get sent to the beginning of the chapter, rather than the specific subsection. When the subsection is "r", for example, I have quite a way to scroll.