The Tenno wasn't seen as a deity themselves, but as the descendant in a long line from a deity. That is a difference.
But anyway, questions on the relationship between emperor and shogun pop up quite regularly.
The following is a selection of past answers, tackling issues of emperor and shogun from various angles (mostly by myself and u/ParallelPain ):
If you feel dissatisfied after reading all of these, feel free to follow up with a more specific question addressing what you feel is missing from this batch. :)