I personally don't rate Otamendi and will be happy if we eventually replace him with a better playmaking defender. But todays poor performance vs Salah isn't his fault.
RCB and LCB in todays 3-5-2 system are basically positions for players with fullback capabilities, i.e. movement, acceleration and ability to engage in pressing higher up the pitch. Pep himself played in a team using such approach, sometimes even as CB or DM, as a coach used it at Barca for a season and occasionally at Bayern, so knows it very well.
The 3ATB+DM system is genuinely self-sufficient defensively and don't necessarily need the presence of wingbacks (like in 'Cruyff diamond'). But only if it includes the players of right types. Regarding the Pool game, IMO the questions should be asked to the coach who placed Mendy too high and exposed Otamendi, basically playing Ota out of position without any coverage.
In the second half Pep has corrected this mistake, switching RCB and LCB and tweaking WBs movement.
Put Kompany or Stones in Ota's place in the 1st half, and the performance would be the same. The problem is that we don't have suitable players for the system, not Ota's deficiencies (as much as I don't rate him as a defender). A player like Mendy, but with better defensive ability, is needed there.