Personally? I'm always positioned in a way to get an out. I don't stick around after I ult, and I predict movement of enemies, because Zyra's skills have delays. The best way not to trade is own the bush you are in, predict where someone on the enemy team is going next, and set a trap.
If you can't set a trap but are fighting on the go, make sure to throw E when you can guarantee it lands, not when someone's running at you (
for instance might Q you or a plant to avoid an E.
Place R where champions Will be, not where they are. If they are chasing you, place it on you. That makes them choose.... either run into the ult/take damage/ get knocked up before they reach the other side...... or back off. Either is good for you.
Also, I generally don't care about my KDA being in kills. I'd rather 8/3/22 than go 20/10/12..... because they got a lot less gold off me, and my teammates got fed too. So..... I often don't run Comet/Aery If they have an assassin that can reach me. I run Phase Rush, or I go Electrocute, and pick up Nimbus cloak/other movement rune options. I do less damage, but I control the map better and more readily.
Personally.... if you look at Zyra's stats, you'll notice she doesn't have a clear cut rune combo. There's at least 3-4 well performing Keystones and every under rune has a good rate of return. The runes I'm suggesting are chosen less, but have about the same win rates.
Still..... as you said, that's because a lot of Zyra's trade..... which isn't always a bad thing on her. A plant army that chunks and kills 1-2 and hurts other enemies isn't a wash. It's usually a win. So..... common non movement runes, although scoring like 10/10 scores or even 2/10 scores.... are still doing their jobs.
But..... I don't think they'll climb as well because that's a lot of lost agency while she's dead.
My build has 487 Move speed WITHOUT BOOTS and without Nimbus cloak being active (and that's on a champ with no move speed skills) If I throw in boots I move faster than most junglers or assassins that would pursue me.
I'm not going to break down my build because it changes. Just saying..... move speed helps if you don't want the trash KDA's.