Interesting... because pretty much every single one of mine has at least some of the living base of the stem under the medium... that's how I bought them and how I've repotted them... I usually bury up too covering the roots that are below all leaves, ensuring the base of all leaves are above the medium
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I personally feel only burying the black, dead looking portion leaves too much root exposed and in my enviroment those will then die off.
In the case of one of my plants that had worked it's way up so the plant was almost entirely out of the medium the sections of roots between the plant and the medium all died off, and the only living sections of root were all below a dead portion... I was quite worried as that left me with only roots that were on their way out. Luckily after a re-pot a bit deeper and treatment with seaweed a lot of new roots have grown which are looking good.
I don't know... maybe I've just been lucky with mine potted a bit deeper, but I've not heard this before about potting them higher