I do wonder what the final dimension of a pellet would be after travelling trough the bore (and perhaps the choke) then hitting an incompressible liquid, however this is how I measure my pellet heads after sizing. First I start with a good digital calliper and check the accuracy with one of the "test bars" from my micrometer set............

I set the micrometer to measure mm and check that the gage reads 0.00mm when closed.
Then I take a pellet, set it's base on my Formica table surface. The calliper has a couple reference marks on the jaws so I'm always measuring the pellet head at the same position on the jaws. Then I SLOOOOWLY close the calliper jaws while moving the open jaws parallel with the pellet. When the pellet just starts to move with the pressure of the jaws the reading is recorded. Here are a couple pics..........
Calliper flat on the table so the jaws close only on the pellet head since the pellet skirts are normally a few .01mm larger than the head.......

An unsized die "B" CPL pellet head..........
The results after measuring a few thousand 8.4 grain JSB Exact pellet heads..........

Notice that all these pellets came from tins marked 4.52mm. I really wasn't concerned that the dimension had an exact 1/100mm accuracy (.01mm= 0.0003937008in), simply that the pellet head fit the leade of my springers without "loose fitters". Careful sorting with an accurate calliper does address the "fit issue" adequately for my purposes. Matter of fact, rather than sorting Exacts and FTTs they tossing the "ill fitters" I opted to take die lot marked and dated Crosman Premiers from the 1250 count boxes and size the heads to either 4.52mm or 4.48mm (4.52mm for my R9 and 4.48mm for my HW95). This way I can shoot almost all CPLs with few "culls" since most CPL heads from my latest die "B" stash measure 4.54-4.55mm.
A few hints measuring pellet heads...........
1. Pellets aren't always round and many vary .01-.02mm in diameter if measurements are taken 90 degrees apart on the same pellet head.
2. It takes practice to get a "feel" for a consistently light squeeze on the calliper jaws. Lead is soft (even hard lead Crosman premiers) so it can deform with excess pressure which affects the reading.
3. Your shot pellets should mimic the bore of your airgun so they should be round within the limits of the bore/rifling geometry unless the impact with the water alters the dimension.
4. My suggestion is to carefully push the pellet through the bore (if possible) which will retain the actual geometry of the bore/rifling.
5. For what you're trying to do perhaps the "holes in a plate" would be your simplest choice. Seems that according to the reviews even "outta round pellets" can be sorted accurately enough to improve the accuracy at the target! Also it seems that "holes in a late" doesn't require any "operator finesse" which is definitely needed when using mechanical measuring devices!