Can this sequence of events cause a commander to be permanently phased out?
I would say that Isamaru does phase back in. Rule 702.25m does not check whether a phased-out permanent would have otherwise phased back in, and it does not in any other way distinguish between direct and indirect phasing, so my interpretation is that it provides an additional way that phased-out permanents could phase back in separate from the direct and indirect phasing described in the other rules.

The situation does change if Alice Donates Isamaru back to Bob before casting Reality Ripple. Rule 702.25m specifically applies to objects that phased out under the control of a player who as left the game. If instead Bob controls Isamaru when it phases out, then 702.25m never applies to Isamaru, and no rule instructs it to phase in, so it stays phased out forever.