From your description it would appear to be a rather unusual set up on several levels.
1) First of all, unless my memory is mistaken (& it's quite possible), a Glowworm Ultracom is a combi boiler. If so, it would be a bit unusual to have a hot water cylinder connected to it. Combi boilers produce hot water on demand when a tap is opened, and so have no need of the time control required by systems with hot water cylinders where the boiler has to heat up the hot water cylinder before you can use it. [Systems with stored hot water usually have a heat only, ie not a combi boiler]
2) For a two heating zone + hot water cylinder, that would require three x 2-Port motorised valves for control (Sometimes called an S-Plan Plus). However, a 2-Port valve for control of hot water does not require a connection to the programmers 'HW off' terminal.
3) Also the CM901 is a programmable thermostat which means that it can control both time and temperature settings. Therefore it isn't normally connected to a separate programmer as well.
Normally I would expect to see:
Heating Zone 1..... Programmable thermostat 1 connected to motorised zone valve 1
Heating Zone 2..... Programmable thermostat 2 connected to motorised zone valve 2
Hot water cylinder..... A single channel programmer connected to zone valve 3, via a hot water cylinder thermostat
Sometimes where there isn't a hot water cylinder, I have seen a dual channel (heating & hot water) programmer used to control the 2 heating zones, except you do have a hot water cylinder, and it still wouldn't explain the HW off connection
I have also seen a dual channel programmer used with two non
programmable room thermostats connected to the Heating channel, and the hot water cylinder to the Hot Water water channel but that wouldn't explain the HW off connection either.
I wondered if the system had once been a single heating zone with a 3-Port valve that had been converted, which might would explain the HW off connection, but it would still need a HW on connection and it's a new build so won't have been converted anyway. All very odd.
So because it's a new build I would suggest that you get the builder to come and explain how it works, or if your neighbours have a similar installation you could ask them if they know.