Hey, I checked if I could solve the compatibility issue, but not without loosing feature in my side.

I think I identified the issue, check this thread:
https://mods.factorio.com/mod/zen-garden/discussion/680ff99f1c864a5aa4284dec

My recommendation, when getting the seeds for icon parameter, check if .icon exists, otherwise use icons[1]

Howdy, 100% thats the way to solve this, I only recently learned that icon doesnt need to exist if the icons[] array is present - opps!

I'll make sure to incorperate this on my next update as soon as I have time. I have acrued a long list of updates and bug fixes to do haha.

Hey, I updated the Zen-garden and removed the incompatibility.
Please note, that If both Alien-biomes and Zen-Garden is active, the collusion-layer count will be reached.
I know this is already a know bug. Have you tried editing the seeds/plants tile restrictions instead of collusion mask? Did not go deeper into your code this time.

data.raw.plant["tree-plant"].autoplace.tile_restriction = tile_restrictions

for _, plant in pairs(data.raw.plant) do
if plant.name:find("tree-plant", 1, true) then
plant.autoplace = plant.autoplace or {}
plant.autoplace.tile_restriction = tile_restrictions
end
end

.208 Checksum for core: 1599024484
2.208 Checksum of base: 2095342242
2.208 Checksum of alien-biomes-graphics: 0
2.208 Checksum of elevated-rails: 755107374
2.208 Checksum of quality: 3594706471
2.208 Checksum of space-age: 2561352795
2.208 Checksum of alien-biomes: 2235899061
2.208 Checksum of quality-seeds: 2144429593
2.208 Checksum of zen-garden: 797994999
2.579 Info PrototypeList.cpp:85: collision-layer counts:
2.580 Info PrototypeList.cpp:87: alien-biomes: 1
2.580 Info PrototypeList.cpp:87: base: 24
2.580 Info PrototypeList.cpp:87: quality-seeds: 70
2.582 Error ModManager.cpp:1758: Reached id limit for collision-layer. The game can't contain more than 55 instances of this prototype due to hardcoded limits of the engine. See the log file for more detail.

Yea unfortunately its the collision mask for the cultivators (biochamber prototypes) themselves are what use those extra collision masks - I havent found another way around it yet, and need one for each type of plant - typically this is only 3 layers, yumako, trees, and jellystems... alien biomes is likely adding in a bunch of plantables, I could go through it and check to see which ones are "worth" growing, but I will need to familarise myself with mod first.

I could write some sort of complicated set parser which compares the tiles between plants and merges same-same collision layers I suppose - perhaps that is a really good idea.

Yeah, I believe you could have a shared collision-layer based on tile restriction set (This could trim alien-biomes many plants into 6-8 biome layer)

If you are interested in an (untested) Grok suggested solution, I am happy to share it.
message me on X @boobleone