Another solution is to us a larger transformer size, and thus be able to implement just one transformer.
I believe the transformers used by Rachio are the standard 24 VAC 40 VA (watts) transformers that are used for multiple applications including HVAC.
If instead a 24 VAC 80 VA transformer is installed, then this is large enough to run two valves simultaneously. Now the wiring can be changed to return to a standard 'one return line' for up to 32 zones.
At first this appears as a nicely elegant solution. The problem is that 24 VAC 80 VA transformers haven't in the past been available as a nicely packaged, UL Listed, with internal fusing, etc, like the 40 VA transformers are. They're often times not UL Listed, not with a nice plastic case, not available until you go up to sizes like 300 VA, and/or don't typically have internal fusing.
If you choose this option, make sure the 80 VA or more transformer chosen is at least UL Listed. As this will reduce chances of fire.
Another option is to change the wiring. So that each 16 zone Rachio unit has it's own 24 VAC 40 VA transformer, it's own return wire for the valves, etc. This is the most straightforward solution if you can do this.