Howdy,
Looks like the neighbor bonus isn't actually triggering regardless of how the plants are connected to each other. I was looking at the underlying chemical-reactor-reactor entity to gauge if the neighbor bonus was triggering or not via the tooltip and checking how much heat I was getting (under the expected amount from neighbor bonuses).
From a basic code inspection it looks like its missing a new 2.1 property called "neighbour_connectable" which seems to be defining where two entities can be considered "connected".
It looks like it should be possible to define the connection points along the overlaid pipe connectors rather than on any of the actual heat connectors too; though I think for properly transferring heat between entities these should probably also be touching? Not really sure what the right "connected" should look like here. This might warrant additional details in the tooltip too for how players should try to connect stuff since the pipes aren't aligned normally.
Sample code exists in the vanilla nuclear reactor's definition.
Also dig the mod, concepts are cool, keep up the good work.