Except that with traditional fx there would probably be more people involved doing the work, plus with CGI, once the model is completed they do not need to recreate it from scratch, just change it's animated sequences, reducing the amount of time and effort, which reduces labor costs.
But building sets is something that has to be done for nearly every series, regardless of what it is, and really with only 2 permanent sets, that is fairly cheap.
While the facade of the Milk Dipper might be real but I am quite sure the interior is all sound stage to make filming easier. Since it's a tiny cafe, it makes sense to build a set with movable walls so the camera has free access.
With shooting begining at 5am, when most areas in cities like Tokyo are a ghost town, that is most likely when the city scenes are filmed, resulting in zero interruption for the everyday population. Also, typically location filming is done outside of Tokyo, in places like Saitama.
Shooting schedules are created to maximize time for actual filming and minimize interruption, so while a switch might happen in the edited episode, filming is done non-sequentially, so for example everything requiring M-Ryo make-up would be filmed all at once, thus reducing the impact of any make-up/costume changes on the flow of filming.
I would not be surprised if the budget for Denou is the same or less than Kabuto, since the ratings drop Kabuto produced and the fact Denou is performing worse in the ratings than Kabuto did at this point last year don't spell good things, since most ratings tend to get lower as the series progresses.