Gary, the answer is yes... For center spark, they have tools to measure bore and stroke without pulling the head. Of course you need access to the area above the spark plug holes for the tool. Both organizations SCTA and Bub use them (SCTA does the measuring at USFRA events).
If you bring your own tool, as long as you can demonstrate accuracy I'm sure they would use it. That is how they came to use the tool they are using now.
The tool is very accurate... every time I have had a bike motor measured it comes out within a cc, +/-. Most bike motors are typically within 2ccs of class limit, and they seem to measure just fine.
If you are 1352 in the 1350 class it will depend... In special construction you are allowed a clean up over bore of .020 or about a half mm larger than stock bore for the motor... if you already are 3mm over stock, you will not be allowed any extra ccs for clean up overbore. The extra cc allowance can only come from the .020 over stock bore. That means a new busa motor at 1352 moves to 1650 class...
So be aware, the limit is the limit, if you are over, you will have to reregister in that class $$ and start over.
This is my experience, the way I read the current rules... when in doubt, contact the scta bike chair for the final say.
Don beat me to most of it....