I think there is a lot of exaggeration going on here. The only thing they announced was, that there will be preloaded lists for the order in which siege engines are built. Now it sounds as if some people think that sieges will be auto-resolved.
We won't be able to breach walls in the scene, yes, but that wouldn't make much sense, or be any fun, would it? Large trebuchets could take the better part of an hour, or more, to load, and would be able to set up at a (mostly) safe distance from the castle. That means operating them is a lot of exhausting work, going on for days, with no real action all the while. Tunnelling is possibly worse. I feel it would be a dreadful chore to do any of that personally in a scene. Much better to resolve that tedious part on the campaign map in compressed time. And loosing some men to attrition during that time is perfectly reasonable. You are laying siege to a castle. That is bloody business, there will be losses, what do you expect?
At the same time, all the exciting stuff will still be there. There will be dramatic assaults, with (smaller) siege engines on both sides firing away, battering rams, ladders, siege towers, all of which can be personally used by the player character. This is where all the action and drama take place, and where it's fun to play out events in a real time scene.
I think their design choices here are perfectly justified. And so I'm confident that the design of the siege engine construction will be equally good, and won't limit player interaction. After all, how many possibilities are there really? You (A) build ladders and rams first if you want to attack as soon as you can, and possibly wait for ballistae and a siege tower if you want support while assaulting. Or (B) you build mangonels (maybe also tunnels and trebuchets) first and assault gear later, if you want to bombard and breach the walls before attacking. And maybe (C) a balanced selection, when starving the place, to keep the defenders unclear of your intentions, and also "just in case".