Yes - ex MY is very good value in PE and has free changes/cheap cancellations - and if you are SG based you can route via Singapore and take stopovers here as suits
I am considering the ex - JHB option as the connection is no extra cost vs having to get myself to KL
One word of warning though - around local holidays the crossings get EXTREMELY busy - 2hrs to cross would be possible. The "second link" is usually better
You can either book a private transfer or take a Malaysian taxi from Queen St to JHB. No Singapore taxi or Grab/Uber can take you.
Budget options would be the bus over the border then bus/taxi to the airport. Or there is a train from Woodlands over the Causeway - which has the very big benefit of it's own customs so no uncertainty on timing, but tickets and frequencies are limited and sell out well in advance for the popular timings