After operating a variety of CNC machines over the years I can say that you should start with Up it’s as they are way less likely to start a fire in most materials. Just remember that using an hour will pull up the hairs on your top layer but will leave a clean bottom layer.
Now with down it’s I wouldn’t use them with all materials. Specifically MDF. MDF is very prone to starting fires especially with added friction. So think about making holes in mdf with a 1/4in bit, there is no where for the chips to go but down and that is like you rubbing 2 mdf sticks together really fast. Poof fire that is now a pain to put out. This can also happen with plywood but it’s not as prone to lighting up like mdf is.
What I love about downcuts tho is that very nice surface finish that you get.
However, if you plan your cuts ahead of time and flip your A-side/B-side (if you have one) than it shouldn’t be a problem.