We lived without 3d high speed machining before it was invented. I think you still get it in 2d style pocketing so you can get used to its functionality.
There were also clumsier methods of doing multiple part location machining before XR4 came along. Only you would know how often you could make use of this feature. It is well worth having if you could use it. But you can always upgrade later on as you can afford it.
So far as capping holes without the surface and solids modelling, you can make simple cylinders or whatever shape you need in your other cad, import it into OneCNC and position it within the spaces you do not want to machine with 3d toolpaths. OneCNC has no requirement that the models be 'solids', as any conglomeration of solids and surfaces can have toolpaths run over top or around.
For 2d type toolpaths, you don't need to cap the holes, as wireframe geometry which you extract from your models (if that is your method) presents itself as boundaries and profiles where you pick the side to put the toolpath on.