I think his defense is sort of:
1. We had a busted accounting system
2. Early on in FTX people had to route dollars via Alameda because banking is hard
3. We accidentally credited those dollars both to Ftx and Alameda
4. Each side thought they had billions to spend / lose (their VC and related spend was WILD), and suddenly, oops!!!!!!
I suspect there's a grain of truth to this, in that steps 1-4 did actually happen to some degree and influenced expenditures/risk taking that the firm couldn't back. Given what's known (for some definition), the upper crew knew about the problem well before the bank run, and knowingly transferred funds from FTX to Alameda. This sort of 'best case' scenario still implies an absurd commingling of exchange and user funds.
It doesn't strike me as plausible that nobody ever questioned the extra billions , and it definitely isn't believable that when Alameda got margin called, they just casually 'sent' some of the double counted billions without taking some time to think "hey, so about these billions".
Also, this doesn't square with Sam constantly claiming that he misjudged whether FTT was good backing - if they didn't commingle/steal customer funds, he wouldn't have cared about FTT collateral!