KiCad V5 has not been released yet; you are using a Release Candidate of some nightly build.
I’m not certain if holes are treated very much different than they have been treated in the past. I created the following post so that I could document for myself how to work through the issues of creating mounting holes.
One significant change to the V5 RC’s is that “creating and reading” the Netlist is no longer required. I have not yet tested NPTH mounting holes since also using a V5RC of KiCad.
If you find anything different from my old post, please let me know! Documenting these things helps every user of KiCad.