Hi,
placing footnotes manually is not a problem. It is about changing them. If you put another footnote in between, everything changes. That is the problem. Pretty messy.
For me starting with new software is like betting on horses. Who is going to win or who is going to run for a long time. Waiting that long for that an important feature can be an indication that the horse is already tired. Not a good sign for me. But I find the rest of publisher quite consistant. My first projects passed the print shop without problems. Unfortunately there is no question yet about bigger projects like books. So I will have to stick to Indesign too.
Where is the fire of Affinity? In any case, thanks so far.