That is exactly how discretionary hyphens work… it’s up to the discretion of InDesign to decide if they are close enough to the container edge to wrap or not and if that is going to help the line spacing or not. Their main purpose is to vanish if the text is reflowed so that you don’t get frustrated about the hyphen showing in the middle of your paragraph.
If you want to force hyphenation just use a regular hyphen and it will wrap if close enough to the edge. If in the middle of the line you could use a hyphen + soft return… but that will most likely render your text very awkward.
Manually tracking each line of a printed document seams to me a bit counter intuitive as if you add a single word you’ll have to go throughout the document all over again. I think you should play with the H&J (hyphenation and justification) options to allows InDesign to behave the closest to what you are doing manually.