A PCB with resin filled and cap plated vias has significantly more process steps, and the hole resin filling machine is also a significant investment.
At an absolute minimum,it will require 2 separate drilling operations,2 separate electroless copper operations, 2 electroplating operations, the resin filling and subsequent linishing operations.
All take time and cost money..
Half plated holes also involve an extra machining stage after final electroplating,before etching ,which not only interrupts the normal production flow, but also ties up a routing machine