You would very much want to run your models through a checker of some form if you're going from rendered models to 3D printing. The creator can get away with quite a bit when it only has to be displayed on a screen. Having re-read your original post, I think I might have misinterpreted your objective. I've used Meshmixer to create pegs and holes to enable flat surface printing of models to be glued together with semi-automatic alignment, due to the pegs. It's often a nuisance, as Meshmixer can get wonky with the re-surfacing around the holes.

When performed in Fusion 360, it's a real breeze. F360 allows you to use a plane to slice anywhere you like and creates a new face on both parts. You then use the separately created peg as a tool to punch holes in both faces. You'd want to have one tool to be printed and another tool scaled up a mm for the holes, in order to ensure a decent fit. I don't worry about scaling, but I make the peg a convenient drill size, say 3.5 mm and then use a 4 mm drill to clean out the created holes.

A good part of learning Fusion 360, as with other programs, is not getting to understand the features, which is easy in Fusion 360, but it's getting the workflow understood.