For cutting holes and openings there are some options:
(a) The vendor (at least ones like Hammond) may offer some customization services if applicable.
(b) There are services that make custom cut front panels and such. If I recall the name correctly protopanel is the name of one common one. Obviously if you want plastic instead of metal panels cut then 3D printing services could also be used.
(c) If you're trying to put holes in the flat end plates of the extruded enclosure you could just ignore the vendor supplied end plate blank and have a PCB made to the same peripheral shape and with appropriate internal holes / slots and use that as your end plate. And/or you could use the PCB as a cutting template for machining the enclosure's metal plate.
(d) you could use CAD tools to design a 2D drawing of the panel to be machined along with tooling guide lines / points for the machining operations. Print that onto something like semi adhesive label stock or whatever and then apply it to the surface to be machined and conduct your machnining by the guide.
Not sure if its the same for all of their enclosures, but Hammond minimum is 25pcs IIRC.
Front Panel Express is another great company that does front panels. I love them!