As to why 'Paragon' should be different... in my eyes at least... a God, truly, is something unknowable, beyond the true comprehension of the race that worships it. That race ascribes the term 'God' to it purely to label something ephemeral, to place a label on the focus of their Faith. So the Emperor as God is to make him apart from, not a part of, Humanity. My Pre-Heresy Emperor is very much Human. A God is feared, a Paragon is admired. A God pulls, a Paragon leads. Humanity acts in the name of God. A Paragon acts in the name of Humanity.
Paragon vs Scientist? Well, that comes down to motivation. Both might be the same person, physically and mentally, capable of amazing feats and the results of those feats advance Mankind. But the Scientist wants knowledge, his creations are either the goal itself or steps towards further creations, further discoveries, more knowledge. That Humanity benefits from what he does is almost a side-effect. A Scientist is driven to answer questions, solve riddles, provide explanations to miracles, produce wonderous objects - to expand the boundaries of That Which Is Known. A Paragon may also do all these things, but the discoveries and the creations and the knowledge are inconsequential - what he does is only judged by him in terms of how it helps others, of how it advances Humanity as a race. When they both make a terraforming device, the Scientist will say "I can colonise worlds with this!"... the Paragon will say "We can colonise worlds with this!".