Yes, theres an exception to this bug. When capturing an AI's asteroid with an Defense Tree with an Flower attached to it and with or without killing the Mine that was created from that tree, will not let the player get an Mine out of that tree after capturing. The flower seems like useless.
But, but - if the capturing of the exact timing, say - the player captures the AI's asteroid at the time of the Mine (re)creating from the tree, that Mine automatically changes to the players Mine. That is, only if the Mine is still intact in the tree and has not been plucked by the AI.
This is what i observed about the Mines, but don't know about the Super Seedlings.
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UPDATE: After applying the update version 2.03, the following fixes were found [while playing DMM 11]:
1. AI can now plant the flowers on Dyson tree.
2. When an player (re)capturing the enemy asteroid having an flower planted on Defense/Dyson tree by the AI, produces an Mine/Super Seedling for the player.
Thanx for the bug fix. Now the game will be quite more challenging 
I might have been wrong, the 2nd time i played it did not work. I will give reconfirmation after few more plays. Sorry.