Yup you can flash between the two as much as you want, however I would recommend a power cycle/factory reset if going from merlin to stock or vice versa.
My personal opinion on the firmware, is that the tweak's on the stock firmware give me the granular control that I want. I am big into open source, enjoy modifying all of my tech to my specific need's, and enjoy the research of learning new technologies. I could spend hour's digging into the open source side of ASUS firmware, or playing around building different script's etc. Point being it give's me a sense of freedom to use my device however I like.
I'm going to use a few playful analogies
Stock firmware = Saiyan
Merlin firmware - Super Saiyan
lol, if you're not an anime fan, here's a comic book reference
Stock firmware = Bruce Banner
Merlin firmware = Hulk
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