Question 1
Why does the boiling tube start off completely full of water?
The right answer is the one marked above.
So that any gas found in it afterwards must have come from the plant. There was no air in the tube to begin with, so nothing else can account for what collects there.
The inverted funnel does the other half of the job: it channels every bubble rising from the plant into one place instead of letting it escape into the trough.