Yes. We do hole drilling all the time with our CNC coding. The holes you have defined in the picture just need to be on a separate layer (or select and code them separately).
We are able to do Outline routing, centerline routing, peck drilling cycles, hole drilling, and any other operation supported by the CNC software. We are mostly familiar with MasterCAM, but other programs should support the same operations if setup properly. We evaluated quite a few CAM programs and bought MasterCAM because of the output graphics (EnRoute was our second choice).
V11 of Alibre provides excellent DXF output, of where you can simply move the linework to a layer, or overlay toolpath linework with new graphics, and constrain it to the existing graphics. We create layered DXF files where we often overlay linework over the existing graphics (as you can only move a line to one layer). Holes we generally just move the graphics to a layer as they do not share lines. We do this extra work in Alibre as the layered graphics will adjust with changes in the model. Change the size of the model, and you can output a new DXF with all the layered graphics in their new location. If you output a raw DXF, you need to re-toolpath the graphics in your CAM program. Even one off output is often faster to layer the graphics than to code it in your CAM program.
Granted your $15,000 cabinet program will automatically create your layered graphics, but then again Alibre will allow you more design freedom to create whatever you can conceive. For stock cabinets the expensive cabinet programs are more efficient. But for custom design furniture and cabinets, Alibre can prove to be more efficient. We have also created standard cabinet models where we can now create cabinets with nearly the efficiency of the expensive cabinet programs.
Vectric has been discussing their next release which will contain nesting, and we hope that will bring nesting into the affordable market. For now, we recommend Alibre Professional (with Configurations) and one of the CAM programs with an ATP or Nesting module (MasterCAM, AlphaCAM, EnRoute ...). We are always glad to spend some one on one time on the phone with other woodworkers and let you know the advantages of Alibre. We own other cabinet software, but prefer Alibre for our custom work.