hi ,
I don't see how your pistons that are flat topped or domed can be waterboxer pistons.

Waterboxer pistons are hollowed out ..like bowl shaped on their tops. 

displacement can only come from bore and stroke of course, nothing about wrist pin location, piston top shape, rod length,  etc.
it is my understanding that the only difference about bore and stroke 1.9 versus 2.1 waterboxer is the stroke is longer on the 2.1 , and bore it the same. 
 Wrist pins are larger on the 2.1 ...I believe , or might be. 
 I have a extractor tool for air cooled oil pressure relief valve pistons ..
and it works perfectly to extract a 1.9 wrist pin, but wouldn't work on a 2.1 as I recall...
the ID of the 2.1 was too large for that tool.   

but for sure, I don't think there are flat topped or domed waterboxer pistons. 
the combustion chamber is in the piston top, not in the heads.
the heads are actually flat bottomed .....not counting the recess where the barrel sticks up into the head.

Scott
www.turbovans.com 
  ----- Original Message ----- 
  From: VWBrain@aol.com 
  To: scottdaniel@turbovans.com ; vanagon@GERRY.VANAGON.COM 
  Sent: Friday, July 02, 2010 6:20 AM
  Subject: Re: vannie info on cranks and radiators needed

  In a message dated 7/1/2010 8:56:32 P.M. Eastern Daylight Time, scottdaniel@turbovans.com writes:
    the cranks are different between 1.9 and 2.1 since the only real difference 
    is stroke...
    they both take the same pistons and barrels..
    it's the longer stroke that makes it a 2.1

    on bare cranks ....don't know if there's a part # or ...could measure stoke 
    ..

  Hey Scott  I have 2 sets of pistons here.  one has a dome top and the other a flat top , the wrist pin holes are different.  1.9L P&Ls  #  025 198 075      2.1L P&L#  025 198 075D      how can they be the same when they are different physical and part #  ??    Now I have 2 cranks setting in front of me  one is out of a 2.1(Main bearings are different in how they lock into place) other is out of a 1.9L   No part # and they look the same.  Dealer gives a different part #  025 105 101A  1.9L  and 025 105 101B  for 2.1 L  all the journels measure the same , laying a stright edge down the center and the strokes measure the same.  It is my thinking that the size difference between 1.9 and 2.1 is from the differences in the piston height and the stock compbustion chambers between the heads.  Bentley only shows that they are color coded but there is no color dots on either of these cranks . I have been working on these guys a long time and can tell an aircooled crank apart just by looking at it. but I can not see any differences in the WBX cranks   later  mark d