The conjuctiva can overgrow but that is more like a layer of semi-opaque skin like in this picture.

Source: http://www.medirabbit.com/EN/Eye_diseases/Disorder/Pteryg/Pteryg_en.htm
The change in iris colour in your rabbit looks rather like “marbling” or sectional heterochromia that is seen in some rabbits. Its not a medical concern.
Uveitis is another situation where you may see changes in the iris to.
Ask the vet to do a pressure test of the eyes if you are concerned about glaucoma. I personally don’t think it is signs of this but I am not a vet, nor do I know the early signs! I do think that now the excess tears has stopped is a good sign.
When I’ve used ointments on the rabbits eyes, Id squirt a little onto the middle of the eyeball then hold the lids out and open as best I could. The ointment would sort of melt over the eyeball. It’s inevitable that some will end up over their skin though. I think you’ll find even if it’s on the outer lid, some will still continue to “melt” or make it’s way back into the eye.