string eval is already flagged as dangerous spot and "use" too

I missed the mention of string eval. As for the use re 'eval';, it's not prevented by preventing the use of use as I suspect you can achieve the same effect without actually using use.

The new thing here is substitution with two "e"-s:

It's really just another way of writing a string eval.

s/.../.../ee
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is the same as

s/.../eval "..."/e
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(without making '"' special).

Do I understand correctly that a single e after the substitution would only be dangerous if the code inside is dangerous

If you consider $1 safe in code, then s/.../$1/e is safe too.