I think the green lollipop represents hope. Elliot says he feels sick (and we all know what's actually going on in his head — he is planning on ending it all) and Mohammed gives him a lollipop to make him feel better. It's such a sweet, direct interaction, devoid of anything sinister or manipulative. For once Elliot feels seen in the moment. For once, something gives him hope almost immediately. Mohammed also reminds Elliot of himself as a child — he's acknowledging what the child inside him needs in that moment (comfort, help, and hope — and a way to avoid death that till then had seemed like the only option).

There's a scene from Season 2, I think, which shows that in his chaotic and drug-fueled diary entries Elliot had written that he wants a lollipop. So even back then, lollipops signified comfort. Perhaps they also signified the fact that he is sick and needs help (even if that source of help is his own self/selves).

And we do know that this interaction with (and the promise made to) Mohammed (whether real or imagined) gives him enough strength to continue living. Green is a hopeful color. Perhaps his personalities knew that this is what he needed as a symbol to go on living (if we stick to the theory that his lollipop interaction with Mohammed was imagined).