Quote Originally Posted by worldofneil View Post
Probably because the gardens are a single object in the game, which contains multiple places to plant. The pots however are likely going to each be separate items and as such have no link to any other game items (so won't be aware of items placed next to them).

I'm also no botanist, but I'm pretty sure that to crossbreed plants they have to be touching, something that'd be a lot harder if they're in separate pots instead of planted next to each other in the same soil.
The plants themselves don't need to physically touch to crossbreed, just the pollen. It's like sperm donation, you don't technically need to be in the same room as someone to get them pregnant, just the sperm needs to touch the woman. Same principle with pollen.