The second case is taking the Purge focus, but choosing the bottom option every time. This is your worst possible civil war scenario, but is the only one to have no technical penalties or officers purged (picking Trotsky still give you that negative modifier). The downside: About half of your territory rebels, and has a very real chance of joining the Axis. Saying no to Trotsky lets you keep Stalin, and may lock out some national focuses on the bright side, you don't lose anyone in the Purge. If you take that, AND take NKVD, subversive activities costs drop to zero Justifying War Goals is technically a subversive activity in the game, allowing you to declare war on anyone in a very short amount of time. Trotsky gets a focus to remove his penalties. It is entirely manageable, as the front size is far too big for the AI to deal with.
Picking Trotsky gives a small civil war run buy Konev, and purges some of your officers and ministers (Zhukov most notably).
In the first case, you will be given a pop-up in late 38-early 39 asking if you want Trotsky to take over, or to have a larger civil war. Mimd the difference between not taking the Purge focus at all, and taking it but choosing the civil war options.