l have instant problems with footnotes in InDesign. There are no options to handle them as you want. An example of issue I have now. I have a text frame on page with title with span of two columns and text with split of two columns. There is text, than new title than text. There is footnote in the first piece of text before title in two columns. I need that footnote to be at bottom of text frame with span for both columns, but there is no way to do that besides manual footnote or fake footnote with invisible real one with span at end of text frame. This makes me mad, so many years of development and such weak footnotes tools!
You have to put them in a separate frame at the bottom of the page without using ID's footnote feature.