Fulgrim is now a creature of the Warp, meaning his mental state greatly affects his physical state.
The virus bomb left no lasting mark on the primarch, but Rylanor's own words, the "denial of (his) magnificence," very much did.
I know (I think) that Rylanor making Fulgrim ugly is a joke, but the entire ordeal left a scar on Fulgrim’s ego. According my knowledge, a daemon prince or primarch can change their form to anything, so Rylanor’s defiance and bruise on Fulgrim’s ego caused him to not regenerate quite right