Appreciate the clarification, thanks
If you're merely transiting in KL, i.e. flights booked on the same ticket with luggage checked to Singapore, staying within the airport transit area and not passing through Malaysian immigration, you are not considered to have entered Malaysia. You will be able to enjoy the duty-free concession in Singapore. Keep all your boarding passes for verification purposes.
If you have to pass through Malaysian immigration and get a Malaysian stamp on your passport during your layover, you will have entered Malaysia and will not be eligible for the Singapore duty-free concession. You will have to declare any alcohol in your possession and pay the applicable duty.