Hi Arif,
You are right about them growing underground naturally. At least, that is how the terrestrial species usually grow. I have learned from others to plant shallowly to reduce bulb rot and to make it easier to watch for rot.
Bill

Dear Arif,
I echo Bill's response... When I pay $$ for a bulb and it's a little "iffy", with a gash or some unexplained discoloration, I sit it very high in the pot. Otherwise, I plant it to the shoulders. Over time, they pull themselves down in the pot.

I know that some much older bulbs have necks just above the soil level. My bulbs planted in the ground are also just above the ground, but their offsets grow underground. (I don't cut the ones down that are in the ground, just pile leaves around them for the winter.)

I think I tend to pamper a limited number and plant them high to keep a watchful eye on them.
Kristi