The suggestion that an investigation could make a meaningful determination of exoneration is widely shared and widely mistaken. Investigators and prosecutors try to make cases for conviction, not exoneration.
As
Alan Dershowitz points out:
"Remember that federal investigations by prosecutors, including special counsels, are by their very nature one-sided. They hear only evidence of guilt and not exculpatory evidence. Their witnesses are not subject to the adversarial process. There is no cross examination. The evidence is taken in secret behind the closed doors of a grand jury. For that very reason, prosecutors can only conclude whether there is sufficient evidence to commence a prosecution. They are not in a position to decide whether the subject of the investigation is guilty or is innocent of any crimes.
That determination of guilt or innocence requires a full adversarial trial with a zealous defense attorney, vigorous cross examination, exclusionary rules of evidence and other due process safeguards. Such safeguards were not present in this investigation, and so the suggestion by Mueller that Trump might well be guilty deserves no credence. His statement, so inconsistent with his long history, will be used to partisan advantage by Democrats, especially all those radicals who are seeking impeachment."
It's possible that an investigation might uncover evidence that conclusively supports exoneration, but the absence of evidence for exoneration in a prosecutor's case is not sufficient to determine that exoneration either is or is not due to the accused. "If we had had confidence that the president clearly did not commit a crime, we would have said so" only tells us the prosecutor's attempt to make his case, while failing, did not also produce a clear case for the defence. If investigators/prosecutors in the course of things were routinely able to reliably prosecute or exonerate - and bound by law to do so - I suppose we wouldn't need defenders.
Just to be clear, there is no "but for" with respect to findings (eg. a finding that a crime was committed). The "but for" (OLC opinion) applies to taking a president to court. There's no conflict between the statements because Mueller's claim is that he failed to make a finding that supported a prosecution, not that he was prevented by law or policy from making such a finding.