#2 is correct (or more correct). #1 is incorrect (or less correct), but it will usually be understood by most listeners as meaning the same thing as #2.
In other words, this answer is a bit pedantic - most people will not notice or care about the difference, in most contexts.
This is correct:
This degree of freedom in design can either lead to energy efficiency or lead to better space utilization.
(And you could use a different verb in place of the second "lead to": ...can either lead to energy efficiency or enable better space utilization.)
This is also correct:
This degree of freedom in design either can lead to energy efficiency or can lead to better space utilization.
The positions of either and or control (at least suggest) their scope.