Peppers don't root from the stems as easily as tomatoes do, but there is nothing wrong with planting them deep. I always do.
The reason for not planting things like fruit trees or roses deeper is mainly because they are GRAFTED to a hardier rootstock. If you plant too drrp they could root from the tree stock and not be hardy. The other extreme is also true with trees -- don't plant too shallow. If the top dies, the rootstock could sprout and chances are it wouldn't be something you would WANT to grow.
Carol
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