Note: sí = yes; si = if
Conditional sentences are made of two parts: a protasis (if-clause) and an apodosis (consequence).
Any conditional sentence requires both elements, although sometimes the apodosis is elided because it can be deduced from the context. However, if this is the case, the sentence is still incomplete for it's lacking the second part, and this incompleteness is expressed in speech trough intonation: generally (although not always), the tone will rise towards the end of the sentence. This happens especially if the speaker intends to say that he/she is somehow questioning the protasis is real or appropriate. See the example below:
A: ¿Puedo salir esta noche con mis amigos?
B: Si crees que has estudiado lo suficiente.
Here, if B (a mother) thinks A (her son) has not studied enough or that it isn't appropiate that he go out with his friends because he's taking an important exam the next day, she would imply such thing by rising her tone towards the end of the sentence. If that's not the case, and she's just saying her son is allowed to go out if he thinks he has studied enough, her tone wouldn't rise.
So to answer you question, if the speaker thinks you can't make a Death Star out of Legos, their tone would rise. If they are simply answering "sí se puede", their tone wouldn't.
But, what if they don't have any expectations as to whether you can or not? Then the difference between both sentences wouldn't be that clear. Nevertheless, whereas in negative sentences the "no" particle is strictly necessary, in affirmative sentences the "sí" particle is not so. If the speaker decides to make the "sí" explicit, they will emphasize it with their tone:
Pepe no va a ir a la fiesta, pero yo sí voy a ir.
That "sí" is stressed, and so would be the "sí" in "sí se puede". The "si" in "si se puede" would never be stressed. Therefore, it's unlikely to be any ambiguity.
Finally, even though "si se puede" (if you can) and "sí se puede" (indeed you can) are both perfectly grammatical, they don't sound too natural in this case because you don't generally use an impersonal tense to say "Yes, you can", but just "Sí, puedes".