Presuming that by separate PNR, you mean separate ticket and that you understand that this is not a connection,but a transfer between two tickets, the sole question is one of risk tolerance. If you are late to AMS, your onwards ticket will be cancelled by A3 and will retain whatever value it retains under its fare rules. That is likely $0. Thus, you would need to find a new ticket to JMK at whatever the then prevailing price is.

My preference for separate tickets is 2-3x the MCT for connections, but others are fine with MCT or even less. All about what you can afford to lose.