So who's right? What should I code? Shall I make 1000 Combat Routines depend on each user request?
Blindly healing the mushroom will wipe the raid on any difficulty higher than Normal. Most likely tons of people who are Normal and LFR heroes with no clue about boss mechanics emailed you and you obliged without questioning.
The problem - especially with the living mushrooms - is that they need to be healed to 100% at the right time or it causes a wipe. The living mushroom is intended to counter the "Infesting Spores" ability that the boss casts at 100% energy. So the CR must only actually heal living mushrooms up fully when the boss approaches that 100% energy mark (starting at 90% may work). Before then the goal should be to only keep the mushroom alive, as it constantly looses health at an increasing rate. So don't heal it if it is at 70% or more health. Once the living mushroom has been popped by healing it to full once, the CR should try to keep it alive as long as there are Infesting Spores debuffs (
Infesting Spores - Spell - World of Warcraft) in the raid as again it will start loosing health at an increasing rate. You can determine whether or not the mushroom has been popped by checking whether or not it has the Living Spores buff (
Living Spores - Spell - World of Warcraft).
Rejuvenating mushroom works similar, except it is popped once the raid moved to the correct position. I am not sure whether or not it is possible for your CR to only pop it if 50% or more of the raid are in a 10 yard range of the rejuvenating mushroom, but that would be the heuristic I would use to choose whether to pop it or not. Again, once it has popped keeping it alive as long as possible is crucial. You can recognize whether or not it has been popped by checking for the Rejuvenating Spores buff (
Rejuvenating Spores - Spell - World of Warcraft).
That is how the mushrooms need to be handled on Heroic and Mythic difficulty. Right now the living mushroom will be popped immediately which will cause it not to be up when the debuff comes and the debuff will wreck your entire raid causing a wipe.
Short term every Heroic and Mythic raider including myself would appreciate it if you can remove the mushrooms from the NPCs to heal list so they are ignored. If it is easy for you to implement to heal an NPC only if he is targeted or focused, that would work as well. Long term you would have to work towards a more complex logic as the one I outlined above or just ignore it entirely. But don't just blindly heal the mushrooms.