Couple quick things:
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When the user signs up, you can use a workflow to create/populate new questions however you see fit. Same thing with creating a new question – set a workflow to create whatever entries you need.
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You can use a junction table if you want, but in Bubble it’s not required since Bubble has a “list” field that accomplishes the same thing. So that gives you flexibility in how you set things up – but more options also mean more decisions on how to connect and structure things. In terms of the “optimal” way – it really depends on the nature of your app, how much data is in there, and how you will search and display. This is a great discussion on various approaches: Alternative approach to the Bubble’s recent tutorials for list of things