To be fair, that would have required having at-launch encounters balanced for both 4- and 6-character parties.
No, it wouldn't. First, because a system of scaled exp would address the problem implictly. Second, because no one is asking to keep the "double choice" at release (not yet, at least). Third, because no one is asking to offer the encounters in two versions now. If anything it would be a great chance to just see what people pick and how they manage with the current balance, precise to decide what types of fight work better, what could use improvements and retuning, etc.
Last but not least, let's concede that would be the case. They already had different encounters tied to different difficulty levels in their previous games. This would be a big problem now... Why, exactly?
I agree with you that scaled exp is the best way to have encounters balanced for both 4- and 6-character parties. But I don't think the start of EA would be the best time for Larian to try their hand at implementing it (DOS games were party exp, right?) as this adds another variable for Larian to consider. Simply dividing exp between party members probably isn't sufficient for balance; likely there will have to be additional adjustments to encounters (possibly fewer encounters with an extreme # of enemies to prevent overwhelming action economy imbalance)
I assume difficulty levels are implemented nearly last in EA, after the "normal" mode is balanced, the story is fixed, the level caps are determined, etc. Doing it this way prevents needlessly creating higher/lower difficulties multiple times after changing mechanics/etc. Variable party size testing should come later in EA after Larian has determined the exact combat mechanics/surfaces presence/etc.