The extra space has to go somewhere – and you must specify it manually, there is no automatic setting in InDesign.
In particular, it seems Align to Baseline is totally ignored inside footnotes! Which is not regular behavior.
Also, you cannot add "Space Below" to the last paragraph in a note, because it is automatically ignored when at the bottom of a frame (which is consistent with the "regular" behavior).The old dirty trick that works to add a "Space Above" to paragraphs – adding a Paragraph Rule and ticking "Keep in Frame" – does not work because … the "Keep in Frame" button is disabled! (Because of "Rule Below". Making it a Rule Above and setting the offset to a negative value does not work, which makes the phrase "Keep in Frame" actually misleading! Also because I can imagine this checkbox should work for "Rule Below" as well.)
But here is a trick that appears to work.
1. Add a blank line at the end of the footnote. If you thoroughly cleaned up your document, the final line of each note will end with a # and not with a ¶ which means to add a blank line you will need two returns.
2. Set the Line Height of that final return to 0.
3. Now you can set Space Above for the final line, and the note text above it will move up. To easily use small increments, set your rules to points, so use can use the up and down arrow keys in Space Above in the Control Bar.
4. How much space to add? If the minimum space before the first footnote is a multiple of your Baseline Grid value, you can enable "Show Baseline Grid". If not, you probably want to temporarily add a Rule Above to your footnote style and set that to the desired distance.
5. Repeat with a max of one million times (once for each one of your footnotes; although you may get lucky and have more than one at the bottom of a page).
That said: if the line spacing of notes is different from the line spacing of the main body of text, it is perfectly normal and expected to have slightly different amounts of whitespace above the notes. It is far more unusual to have the bottom lines of notes hop up and down across pages.
"That said: if the line spacing of notes is different from the line spacing of the main body of text, it is perfectly normal and expected to have slightly different amounts of whitespace above the notes."
I think this may have actually been the answer I was looking for. The book I'm reading right now goes with footnotes that are the same font size as the body, and consistent space above the footnotes. The footnote space made me self-conscious of the inconsistency in the book I'm designing, but the size of their footnotes also bothered me...