Friebel wroteWhat also happens a lot here is that we've selected a bone, and when using the rotate transform tool in the editor suddenly another bone gets selected instead of the transform tool moving.
This would only happen if you drag to rotate while over another bone or attachment. Once you have a bone selected, you don't have to drag on that bone, you can drag anywhere. It shouldn't be hard to find some blank spot where you can drag with nothing under the mouse, then you can make adjustments without the chance of anything else being selected.
Friebel wroteSo then I use the Tree to select a bone, for example, but when using the rotate tool and click one pixel next to it it still selects a close lying other bone, like an IK bone.
Using the tree to select a bone can be convenient. I don't understand why you'd have problems with the rotate tool though? I have a feeling you missed that you can drag in any blank space, you don't need to be anywhere near the selected bone.
In some cases when you are zoomed in a lot, there may not be any blank space because attachments are taking up the whole screen. In that case if you put the mouse directly over the origin of the selected bone, you can drag there without selecting another bone, even when bones are on top of each other. You'll know if you are over some other bone or attachment because the other bone will be highlighted in white and from the name shown at the bottom center of the viewport.
Friebel wroteIs there a way in the software to (temporary) turn off this auto select method in the editor, so we can select bones by clicking on Tree items and use the transform tools without accidentally selecting some other bone that's really close?
Sure, you can disable bone (and/or attachment) selection in the main toolbar, at the far right. That prevents you from selecting those things at all in the viewport, but you can still use the tree to make selections. It's common to work that way, depending what you are doing.
A few tips:
When using the tree to make selections, filtering the tree can be very helpful, eg to show only bones. enter focuses the tree search box, then you can type to find a tree node. enter again goes to the next match, shift+enter to the previous, ctrl+enter selects all matches, escape clears the search.
You can use ctrl+x and x, where x is the numbers 0-9, to store and load selections.
Also here's an often overlooked tip: you can navigate through your previous selections using page down and page up. It's very common to need to go back and forth between selections and these selection history keys are super convenient, allowing you to avoid making the same selections repeatedly and without using your selection hotkeys.
