I got some sorta-data and I'm not convinced damage or tool level plays a role in seed drops. PlantEverything seems to be making it so that you can get upwards of 4 seeds back for each beech tree. The mod makes it so that you get a max of 2 seeds per tree, but the tree looks at the loot table twice and it can double-dip in the seed drop and give you 4. I'm not sure if that's how vanilla does it, but it seems to give you the same upward trend vanilla does.

'Must have been getting some weird RNG because seed yield has been trending upward whether I use a bronze axe, a flint axe, or other trees to harvest trees.