Its fundamentally different. Science doesn't ask you to accept unknowns on faith, its provides evidence that there is something we dont yet understand and that evidence has predictive value.

If science operated like religion it would say "We dont know what dark energy is, but you have to accept it or your wrong".

Instead the argument is "Hmm... our current best understanding of the universe is lacking, when we add in these extra variables many of our predictions go from wildly inaccurate to nearly accurate. There must be something going on here we cannot observe, so lets call it "dark"."

Dark energy is "Wow, there's a factor at play here that we dont understand, without it our equations do not predict what we see, with it the equations are very accurate. Additionally we can predict multiple different things with this."

And the most important part, as soon as there is evidence that refutes the Dark Energy/Matter hypothesis scientists will quickly (over a few years, a decade at the most) walk away from it. Versus religious systems take centuries for people to shift their beliefs.