Dutch travelling South East Asia, but flies back from Beijing. What to do?

I'm in China right now, but do some travelling (40days) from 12th March - 18th April in Malaysia and Thailand. I fly back to Amsterdam from Beijing on April 20th. So for those 3 days (April 18/19/20th) I need single entry L-visa. Is it the best idea to get my visa on the day I arrive in KL (12th of March)? And if yes, at what day can I get my passport back?