Well I'm bit unsure can I use Red oob and "imagine" it to be separatist oob or has anybody done "special" oob for separatists? Or is Russia oob better for that purpose?
If you play both sides with the same OOB, then you get the "rebel" flag for player 2.
Or you could make a custom red OOB. For scenarios, you can use the allies feature for adding Russian kit, your choice of captured (same flag and leader ratings and names etc) or allied.
But if I play generated battle/campaign as Ukraine, is it better to use just same oob (Ukraine) for opponent or is Red oob better (according news sources separatists have newer and more modern equipment because Russia's aid) for that?
Red v Ukraine in 2014/5? that gives battles in in either of Ukraine or Byelorussia). As a quick test run in the battle generator would tell you.
So - if you want to treat Byelorussia as 'rebels' then that may work for you. And you can always edit the Red OOB to add in kit you think the rebels should have from the Russian OOB.
Look here a good page http://wio.ru/anti/15-02-b.htm
with separatist equipment photos and also some destroyed Ukrainian vehicles used against rebels. Photos are collected by months so is good start to build separatist OOB. btw many improvised armoured trucks with various plates on booth sides evidence on photos - looks like civil war in Libya to some extent.