Perhaps it would be helpful to think of isolation in terms of the bird on a power wire. As long as the bird is touching only one wire, it is safe no matter the voltage within the wire itself. Sharing a single wire (commons) between multiple controllers, is like multiple birds sitting on the same wire. As long as birds are leaving each-other alone, we can have peace and quiet.
Isolating commons, such as with your original configuration is like shooing one of the birds away when the second one needs to land on the wire. Benefit of doing this is mostly superficial (useful only in case you power supplies may cause an issue).
The reason for recommending original power supplies, comes to us knowing that Rachio ships supplies with a good isolation from the mains. That just means that there is no voltage offset on the output which could be mismatched relative to another supply.
48V consideration comes from interconnecting a second signal, such as Master Valve without an isolation. In this case current would be generated in Supply A, travel though the M connection to Controller B and cause a voltage relative to a shared commons. Whether this voltage is 24V or 48V depends on the phase of the Supply B relative to supply A. If the phases match, voltage will be 24VAC maximum, if they do not, voltage could be as high as 48VAC when both controllers activate M output at the same time.
NEC actually already shares commons, aka Neutral, between phases & electric loads. As far as their coverage of low voltage circuits (such as 24VAC irrigation system), they are mostly hands off, as long as you are sure that the lines are, again, isolated from the mains.