I am not 100% certain but it sounds like you should be able to play any character in any scenario aside from two possibilities.
First, they have stated that there are some scenarios where certain player characters function as NPCs.
"Bloodletting" (Scenario 2) features a non-player controlled Otis who knows where the important medical supplies for Carl are. Survivors will have to use Stealth again to navigate an overrun school, attempting to find the necessary supplies and a way out before the bell rings! - from update 6
As that is the case and if you only owned the expansion and base game you'd have to be able to play characters from the base game in the expansion to play up to 4 (unless it's weirdly a 3 player max scenario), so I'd think it would be work the other way as well.
Secondly, IMO since there are certain scenarios with special rules (Rivals, Strangers, etc.) that there may be certain characters with abilities that may be more or less useful in a given scenario. But that is purely speculation on my part.