Yes you can remove the pistons leaving the crankcase in the frame, that said and has been mentioned above your issue could well be just a sticky ring/s.
The fact you've run the bike, tested it, got low compression on 1 cylinder and I assume re started the engine after topping up the oil and got a higher readings all round. Suggest it is/was indeed sticky rings and by running the bike has freed them all off giving you healthy readings.
I would give it a good spirited run, revving to 7, 10, etc working towards the red line in the lower gears for about half hour. Allow it to cool and retest if the numbers hold up, you're not burning/using oil outside the spec, forget about the issue.
I would also mention, Fazers as a rule providing they've been maintained correctly, don't suffer bore/ring issues, if anything it's more likely to be a leaking valve/s. But again as a rule anything below 50k would be unlikely, as the rarely need shim adjustment below that mileage, even above that figure they don't go out much with normal road use.
