IF the filler is a different color, it will look off even under the paint, but it really depends. if the door is hollow and made of metal, then the fill will not look as right, if it is solid and made of mdf, then it should look fine as youll be able to sand into the material. IF there are filled holes taht are large somewhere in the apartment (I assume its an appartment) point them out. LEave the dents in the door and claim they were there and hope for the best, otherwise just fill it and work it out as best you can. IT should look fine, if they even notice.
Yeah I honestly don't think they'll notice. If they do, I'll play dumb and point out the other fucked up, half-assed shit in this place.