Partly because building cars that match all together makes production easier, so requiring something else would be reflected in the final price. Partly because the Midwest has gotten a year or more of use out of their coach cars, while California waited quite a while with nearly complete trainsets out of service and a capacity crunch. Partly because Via's entire order is less than a third of the Next Generation Passenger Car order, so "batching" isn't as noticeable for VIA. Also, I believe Via only ordered Coach, Business, and Cab Control configurations, no cafe cars? Partly because Brightline now orders one type of car at a time for their expansion orders, and couldn't start until all 20 initial cars were delivered. Partly because Brightline also doesn't run a cafe car and also doesn't have cab control cars - just three types of rolling stock for the whole operation.
Edit - I read your comment as criticizing Amtrak Midwest's delivery order, not the car configuration.
Trainset maintenance takes facilities set up for it. Trainsets reduce flexibility to change consists and to include Horizon or Amfleet cars in the consist, so adjusting for a holiday period or in response to changing demand is more difficult. This way they aren't committed to a maximum length or a fixed consist, they're able to mitigate the equipment shortage by running married pairs and individual cars as they were received, and they can mix in Horizon or Amfleet as required. Finally, looking towards the future, they aren't committed to one Venture fleet either - they could buy any standard height floor passenger rolling stock to expand Midwest service. Bombardier multilevels, a future California/Long Distance derived transition coach (that one is logistically more complicated), overhauled ex-NEC Amfleets, or a competing single level design.
Since they got seventeen trainsets worth of equipment but not enough to run every trainset at six cars long (and there's already another state dipping their toe into the pool, plus Michigan probably will want more than three daily trains on the Wolverine once the improvements are done, plus...) it's pretty likely there will be a followup order of something in a few years, and in the interim a mixed fleet with the old cars is likely to persist. And they knew this when ordering, at least in broad strokes.
One thing that I don't understand is, if you are buying train sets to give your riders a consistent new experience, why would you not require things to be delivered as trainsets instead of getting the order delivered as a smorgasbord of cars in random order. bot VIA and Brightline took the approach of getting full train sets delivered at a time, as is California (mostly). But I suppose Midwest and Amtrak together have their own approach.
