I think as long as we are not purely duplicating the brain, there would always be something different (by definition of not duplicating). The question becomes then the relevancy of difference. I think there is some plausibility to the idea that some "formal" elements of the brain associated with cognition can be simulated in machines, but would that be "sufficient" for "understanding"? This question is partly hinging on semantics. We can choose to define understanding in a way such that it's fully a manner of achieving some high level formal functional capabilities (abstracting away from the details of the concrete "matter" that realizes the functions). There is a good case to be made that perhaps it's better to think of mental states in terms of higher level functional roles than "qualitative feels" (which is not to say there aren't qualitative feels, but that they need not be treated as "essential" to mental states -- the roles of which may as well be realized in analogous fashion without the same feels or any feels). If we take a similar stance that the point of having or lacking phenomenal feels (and phenomenal intentionality) becomes moot because all that would matter for understanding would be a more abstracted level of formal functionalities (which may as well be computational).

If on the other hand, we decide to treat "phenomenal feels" (and "phenomenal intentionality") as "essential" to understanding (by definition -- again a semantics issue), then I think it's right to doubt whether any arbitrary realizations of some higher level abstracted (abstracted away from phenomenal characters) behavior forms would necessarily lead to having certain phenomenal feels.

Personally, I don't think it's too meaningful to focus on "phenomenal feels' for understanding. If I say "I understand 1+1=2" and try to reflect on what it means for me to understand that, phenomenality of an experience seems to contribute very little if anything -- beyond serving potentially as a "symbol" marking my understanding (a symbol that is represented by me feeling in a certain way, an alternatively non-phenomenal "symbols" may have been used as well) -- but that "feeling" isn't true understanding because it's just a feeling. Personally, then I find the best way to characterize my understanding by grounding it in my functional capabilities to describe and talk about 1+1=2, talk about number theories, do arithmetic, --- it then boils down to possession of "skills" (which becomes a matter of degree).

It may be possible that biological materials has something "special" to constitute phenomenality infused understanding, but these are hard to make out given the problem of even determining public indicators for phenomenality.