I think you are giving it to much importance to this, first we know her mother is dead, this was made to have Henry and Violet bonding, over having parents that died and is also Disney theme, the parents always die and would not fit in now starting to bring dead characters again, we all know what happen to marian.
Second, They wont go back to Camelot to tell Her father story or they wont go back to land without magic story. They insert that line, (that contradicts the S5A where her father didnt liked Henry at all bc he was from other world and a writer and his daughter needed to end with some Knight and hero), to explan why Violet may be seen next season and at the same time to say that her father didnt abandoned her in SB by going with camelot people. Is simple, doesnt have any other meaning besides that. This information will be forgotten or retcon( if even has any meaning) next season.
Third, you actually think with so many stories now, they will actually go back to Malificent and Lily so soon? Yeah bc at this point their story is over, unless they decide to retcon and say her father is someone important, which now with a whole group of new characters available i dont think so, because lets be real they gave up on Aurora, Mulan bring back philip story, that had way more sense to explain, yet they said already they wont show that.