Max, I'm sure the first folks who heard Colonel Powell's lectures about the discovery of the Grand Canyon said the same thing (recall he lost most of the members of his group to various incidents). There's certain penalties that we "explorers" or early adopters have to be able to deal with, then again having conquered them we wear them as badges of honor. In the final analysis I didn't really have too much trouble thinking of inches as mils but yes you do have to take it into account.
I have heard good things about Rhino3D but I also recall hearing that's about $1K, you pay your money and you pick your poison. I do know I got SketchUp to deliver a functional two-piece gauge enclosure with a twist-lock front. Nothing new is ever easy.
I did my first actual 3D parts a couple years ago and I used regular SketchUp version 8. I believe I used the su2stl.rb plugin which USUALLY works OK, there's a webpage about it if you have problems. I actuallly got usable hardware first time using Redeye as the service bureau. I would however give two pieces of advice. One has to do with scaling, you need to bear in mind that SketchUp is only really written to work well for the scaling architects would use, the tools DON'T work particularly well for small things like enclosures so you'll need to scale up the drawing by 100x or even 1000x while you're editing it so at the very LAST step you scale it down before export (which of course works flawlessly). The other is you need to download a REALLY GOOD .stl file viewer and learn how to use it. The reason is if you "drag" one part to be "adjacent to" another, it may LOOK LIKE the two components are "touching" then if you have it made you find they come out as separate parts, not such a great result if you're paying hundreds of $ for a prototype! (I guess you're thinking about having your own machine so failure comes relatively cheap but our time and materials are worth SOMETHING.) It was actually the manager at Redeye who spotted and fixed the problem for me, again showing there IS value in working with folks who know what they're doing! I would also wholeheartedly recommend the same book I bought which appears at the following link to help you understand the various RP processes and services available:
Do not worry, your primary MCAD package should be able to handle 95% of what you want to do. Once you get into the more nuanced issues, is where you start wanting to have a secondary MCAD system. Most of my experience comes from designing wind tunnel models and composite rotor blades. These are areas where the small stuff counts. Geometric deviations of ±.002" on a wind tunnel mode was considered a normal profile tolerance. We once lost many thousands of dollars because a MCAD program interpreted the geometry improperly on import and caused things to be misshapen by ±.020.