How can I seal subfloor gaps before adding a substrate?
If the 1/4" to 1/2" gaps will be covered with baseboard and shoe molding later, then strips of 3"-5" wide plywood, wrapped/covered in a plastic painter's drop cloth, wedged into the gap will create a fairly tight seal until the leveler dries.  

Shims between the strips of plywood and the wall (with the wider part of the shim downward; narrow end up, so the top edge of the plywood can lean against the wall...if it wants) will help ensure the plywood is snug against the subfloor.  

Even if a little the plastic somehow gets stuck within the dry leveler (which happens), a cutting blade can trim it.