In this context, saying 'just there is difficulty creating it' doesn't make sense. It sounds...a bit wrong. 'just that...' is like saying 'but' in this context. It's sort of like 'only' or 'although'. Assumes in this context means that 'it' is supposing or presuming. 'takes for granted' as above is not correct.

"assumes" here means "supposes", "takes for granted", and the rest of the argument is based on this assumption. And about "just that", it could be said "just" too, as there comes a noun clause after "just" and "that" as a subordinate conjunction can be omitted.

Assume: To arrive at a conclusion without sufficient evidence. "Just that" could be replaced with ", but" in this instance as it shares the same purpose.