Just "because it was logical" I understood the compression ratio to be the compression from closing the last port opening to TDC. However, I do remember a discussion in the early 1970s, about the time that Yamaha engaged Queen's University Belfast to dynamically re-engineer the porting of all the suck and blow phases, using the gas dynamic technology available back then. They considered that the intake charge from atmosphere was defined by the stroke below the closure of the intake port, when an engine was tuned so there were effectively no losses down the exhaust port during transfer. So using exhaust back pressure and exhaust reflected shock waves to stuff exhaust back into the combustion chamber they almost eliminated losses of intake charge down the exhaust pipe. But also they contrived bigger and more numerous transfer ports, etc, reed valves, and exhaust valves so that the performace increased dramatically over the next decade. Disc valves really developed during 1950s 2 stroke racing did a similar thing on the intake port to maximise the initial charge intake, timed differently to a simple piston port crankcase intake.
Therefore the initial charge volume - theoretically - is the voume of the stroke of the piston from disc port closure to BDC, plus combustion chamber volume, divided by the combustion chamber volume. But this is only effective if the exhaust is suitably tuned, otherwise the volume of charge lost down the exhaust port before that closes, means you could be running at your 3.6 or lower... I think it is covered in the book "Tuning for speed" - by Phil Irving - and used by many motorcyclists in the 1960s. Also Austin Rodgers book -chapter 3 - search the web for "disc valve tuning 2-stroke engines".
I had a race tuned Yamaha LC350 that pushed 17:1 compression on the gauge at kick-over. Needed Avgas to keep the pre-ignition under control. After burning away 4 pistons I used a cylinder base spacer to drop compression to below 15:1 when it was good with 98 octane and octane booster.... I saw 11500rpm and still pulling in top gear one day, as the highway developed bends, and it seemed that the traffic had nearly stopped. Silly me!