The modern plastic shotcups will fit down your 16 gauge barrel, but they probably won't seal gase. Because those plastic wads go into plastic casings, they are often actually 17 gauge in diameter, and when you try to use them in brass casings, or in a ML shotgun, the cups are too loose in the barrel to seal. You can use an OVERPOWDER wad under them, and sometimes get pretty good patterns.
I would suggest returning them, and ordering the correct wads. Always measure the bore of your gun. Then order the correct sized wads. The wads should be slightly oversize in order to give a good friction fit. Check Track of the Woff's site on line, to see what the wads look like, and what they measure. That way you can order the correct wad you want. I can't tell from your last post if you are wanting an OP wad, or a cushion wad, or a Over Shot (OS) wad for that 16 gauge.
There are some prelubed cushion wads on the market that appear grey in color- almost grey blue. I have some in 20 gauge. I use a 1`9 gauge OP wad, then put down a 20 ga. prelubed cushion wad, then a 19 ga. OS card, the shot, and another OS card to keep the shot in place. Because the cushion wads expand when they collapse under the pressure of firing, they lube the barrel just fine. By using the small sized cushion wad, its much easier to load them down my barrel. I don't need a hole in them to let air escape. With the OP and OS cards, I do need to put a hole in them to let the air escape, or otherwise fight the air pressure under the wad pushing back on the wad and my RR as I am trying to seat the darn things!
Yes, you can use a chronograph with a BP smoothbore. If you are trying to test shot loads, I suggest you make a package of the shot, but making a tube the size of your bore, enclosing the shot at both ends, so that you have a " slug " of shot the same weight as you want to shoot. That way, the shot is not going to spread out and damage any part of your chronograph. Yet, you get the MV of the load of shot you want to use, in combination with the powder charge you select, and the loading components you intend to use with the shot charge. The only thing different is that you enclose the shot in a paper " Cartridge" so the shot does not begin to open up, and pose a danger to your machine or screens. Set the chronograph 15-20 feet from the muzzle of the gun, and shoot off a rest so you don't flinch and shoot the machine. When You have established the velocity and determined how to load the shotgun for consistency of velocity, shot after shot, then go to the patterning board, and test for pattern sizes and any other problems. When you finalize a load at the patterning board, go back and run it over the chronograph, packaging that shot again, to verify the velocit. Some guys wait until they have a load that patterns well before they run it over their chronograph to get the velocity. Since I think you get better groups in a cylinder bore gun if you keep the velocity below the Speed of Sound( 1100 fps) I think knowing what the velocity of a load is before spending time counting holes in paper targets to establish the pattern makes more sense.
I am sure that other's opinions will vary.