Due to flyertalk I stumbled across this fee as I had planned LAX-TPE-KUL-BKK then HKT-KUL on MH. Called PE line and was told yes there was a fee and she said it could be up to $500 per pax. Gave me the MH line to get the exact amount. Asked MH agent about surcharge and without hesitation said yes they do collect this. She looked at the routing I gave her and gave me the price of $261 per person, or $1041 for my family. I don't think so, even though I love MH. Asked for quote for only TPE-KUL-BKK and HKT-KUL so I might try CI to TPE and price went down $500, still too much.
Anyway, I found that if you go to the MH website, start a new booking for the flight you want, select the full flex fare then hit next. Then select the details link under "TAX", and look at the YQ coded tax "Admin fee, Fuel (where applicable) and other surcharges" and this is the price I was quoted exactly. Tried the three different combos of flights I had asked about and the price was always exactly as quoted.