Mueller refused to make a call on obstruction because he wasn’t able to satisfy the legal standard, but he doesn’t think the legal standard is the only or most important standard when it’s the POTUS.
The standard for conviction in a criminal trial is “beyond a reasonable doubt,” often quantified as “98%.” The standard for an indictment is “a preponderance of the evidence,” or “51%.” Given the now-famous OLC opinion, to indict the POTUS, Mueller probably needed to reach 110%: incontrovertible proof on multiple counts.
Mueller wasn’t able to uncover enough evidence to reach the 98% standard. Instead, he probably made it to 85%. A big part of the reason he couldn’t get further is that many of Trump’s confederates stonewalled the investigation by claiming to have forgotten everything. It’s not credible when every person who attends a meeting claims to have forgotten the entire thing: they’re all lying, which is evidence of consciousness of guilt, which is strongly suggestive of a crime.
So, experienced prosecutor that he is, Mueller looks at the missing 15% of evidence and recognizes that it’s missing because Trump is a regular mob boss, and he and his confederates have been following regular mob SOP: do all the crimes, but avoid making any explicit statements, giving any overt orders, etc. The 15% that’s missing is not proof of innocence, it’s the hallmark of organized crime.
Barr and Trump, and now Flood, want to force Mueller to apply the regular justice system rules, which require rounding 85% down to 0% and a clean bill of health. Regardless of what he can prove, Mueller is probably certain that Trump is guilty of many serious crimes, and that Trump & co are desperate for Mueller to play ball and follow through with the standard “rounding error.” Mueller doesn’t want to see Trump get away using the same cheap tactic that vanilla gangsters rely on every day.
This is why Mueller refused to make a “traditional prosecutorial decision.” He can’t satisfy the legal standard, but he knows the POTUS can be tried by a political process that is not bound by those stringent rules – and rightly so. Everything Barr has done since he took office has been an effort to rush us into that rounding error. Trump has acted on the presumption that the rounding error would carry the day, the way it does in run-of-the-mill criminal cases. Now Flood is in on it, too.