Very hard? Not really. I just had to do all the steps in the batch file manually. Anyway, if he wants to keep original double partition layout, then he should set system 1 as active using either Mi Recovery or CWM and then install back TWRP. But then another 600MB gets unusable. So I pretty much see your point in merging partition table to MM layout (I've done it myself).It's because you're on stock partition. You have to flash extend partition zip. But i recommend you to flash MIUI MM via Mi Flash. And use CM13 instead. Because once you extend your partition it's very hard to get MIUI MM partition which is now used by all Marshmallow ROMs. You can go to Mi3 General section and search for instructions or open a thread to ask there.
MI3W 64GB/Tapatalk