You will always end up with some damaged roots when repotting. As for fine rooted types, anything bigger than fairly small bark pieces will be extremely difficult to extricate from the roots without breaking many. So, I do recommend a finer bark mix - shouldn't be excessively fine tho (I like Gubler's fine bark mix), or coconut husk chips mix. You can leave some old bark clinging to roots, so long as you have got most of it.
I've sometimes had that problem, with new root tips dying after repotting - the good news is that when the plant is in root growth mode, there will be more. You can definitely wait til the new roots are longer than 1/2" tho.
Many orchids do have that somewhat vertical growth habit, and some of the Onc alliance very much so! You can leave that new growth above the media a bit. I try to avoid burying old growth in the media, but have done it on occasion without any problems arising from it - could depend on your climate if it may become an issue or not. It's probably preferable to angle the plant somewhat, so that new growth is at least closer to the media, without burying older growth much.
Most roots will find their way into the media on their own.