If German troops shot down a plane, Berlin would have to answer for that, even if it was a mistake. The same holds for Washington, for Ankara, and for every other nation's troops. So if Russian troops shot down a plane by mistake, Moscow would still be responsible.
The separatists aren't proper Russian troops, of course, but since the separatists are exclusively supplied, equipped, and directed by Moscow - do you really think they start any major military operations without getting Putin's okay first? - there is a similar, if lesser, degree of responsibility here.
Direct control is not necessary for responsibility, and neither is a direct order.
Yes, they start without any Putin direct command, because there is no line of command in most of pro russian military. I can give you videos where you can see them fighting each other, who is in command and similar in the past.
If someone gives them weapons it doesnt mean a lot. It is a responsibility , but it is not direct, and it is 100% same as what USA did in syria and other countries, with supplying them, giving training and similar. Both are responsible indirectly. But rebels are NOT russian military, and cannot be considered that in any way or form as you tried to say it in your post.
Also your comment on that a country will need to answer for shooting down a plane and that it holds true for every country is very naive that you think like that. It matters a lot who shoot down a plane, because depending from country , consequences will be different as you saw in the past.