You can do without "in" but there is a slight difference in meaning.
"As in" is a phrasal verb which means "which is" or "which means"
1. I'd say 'Manager Tom', as
in a nickname given to Tom.
2. I'd say 'Manager Tom' as a nickname given to Tom.
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For (1), please see:
The ‘h’ in honest is silent, as in ‘hour’. [Oxford]
So for your sentence, I'd say something like this (which makes more clear to me):
I'd say 'Manager Tom', as in a nickname 'Powerful Manager Tom' given to Tom.
When "X as in Y", that means X is part of Y. That's how I understand it.
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(Update)
Ah, I think that the structure of your sentence is more like this one:
Repeat these five steps, as in the last exercise. [Oxford]