Fractional Captain reported the nonstandard threshold markings and lack of lights along with the active construction and inoperative PAPI equipment at VNY led to a very low approach.

Narrative

Landed on Runway 16R VNY. NOTAMs stated nonstandard markings on 16R. Also north 2000 feet closed. The PAPI was NOTAM'd out as well. There supposedly is a PLASI" but that was nonsensical as well and didn't display any useful information. Also the ILS is out and only a VOR B approach is available which we can only use for reference. In my opinion there is no discernible threshold markings or lights. The markings are so nonstandard that they are dangerous. On final I had to ask my co-pilot where the threshold was. All I could make out were what appeared to be aim point markings. He had been there recently and described to me what to aim for and where to land. All appeared ok when crossing the end of the runway until I saw that there was a raised marked off square that was colored orange with chevrons. Also there were workers on either side of this box on the side of the runway. It appeared I was flying low over the box so I disconnected the autothrottles and applied a little extra power to float over it. It felt too low for a go-around at that point and with the situation; it felt safer to just give the power a little juice to get past the raised box.After we taxied in and disembarked the passenger an Airport Operations vehicle pulled up to the plane and an official requested to speak to us. He said although we landed after the threshold we were very low. I explained everything to him that I just described. He said the FAA signed off on everything but to me everything is so nonstandard there right now that it is dangerous. Again we could not make out any type of threshold and without a useable PAPI and only a VOR B approach that we can really only use for reference it's just ridiculous to me.Suggestions: They need to make the threshold markings and lighting visible. They need a useable PAPI or VASI. To me the project they are doing on Runway 16R at VNY has rendered the runway practically unusable."