Well many Scylla will have some 1AP attack not close range or mindfragers. If there’s armor problem and as aiming less armored parts is tricky with close range, it’s not worth it. Wait at least have the pistol or even the SR.
You may also use the Synderion Sniper Rifle, the Athena, which deals 15 paralyze and 10 damage with, off the top of my head, 40 armor penetration. Will be a much faster way of stunning her and you can aim with that. However, that also means a lot of extra carry weight for one or more of your soldiers when you are going into an “Extreme” difficulty mission.
My recommendation is to do it in a citadel. It is very easy to sit in your spawn area and snipe down enemies as they are “alerted” to you and engage your soldiers. In this manner, you do not need to worry about your encumbrance. With any luck, the Scylla will be one of the last enemies to be “alerted” to you, so you can then focus much of your fire with Athenas on her.
You need do at least 1 damage so the paralyze effect is applied. With long range and aiming you can aim the right part. With close range it’s a bit more complex, it depends of soldier position and Scylla facing, I don’t know any formula for that, the mysterious mechanism will hurt sometimes a part for no damage (too high armor) then no paralyze, or sometimes it will hit another part for some damages and paralyze effect.
Not true, what you missed is that you have to kill all the OTHER enemies if you are going to capture the Scylla in a Citadel. That means all the EGGS. Citadel capture was my first actual capture of a Scylla so I know it does work.