The RT loop is one place where you can remove the link and replace it with a stat to act as a switch across the two contacts.
The clock will be another place where it is wired into two different contacts. Again the clock acts as a switch across 2 contacts. It would be possible to remove the clock from it's 2 contacts and put a programmable stat in it's place . This would make or break the 2 contacts for clock, but you would leave the RT loop in place.
Basically, the two sets of contacts (RT and clock) are just two breaks in the same wire. Current comes to clock contacts > if they are looped or the switch for them is closed, current goes on to RT contacts. If RT contacts are either looped or the swich is closed, the current continues to boiler electrics and turns boiler on. If either or both sets of contacts are open, the boiler stays off.