Perfect sense. One knob is the output temperature of your hot water for washing up etc. That'll vary between about 50 and 60. The other knob is the temperature of the water in the radiator circuit. That knob'll change the temperature of the water in the closed circuit serving the rads... BUT thermostatic radiator valves on individual rads can 'throttle back' the flow so a given rad can be maintained cooler than the others if needed.
The timer thing on your boiler controls when the boiler will 'pay attention' (be governed by) the thermostat in the hall. Outside of these hours it'll just be 'off' / ignoring it / only giving you hot water for washing up IYSWIM.
For greater control, you need a programmble thermostat - this will combine the features of the timer (controlling when stuff happens) with the thermostat (controlling how hot the house gets) so you can set, say, a similar program to Flutterbee: toasty in the early morning, a little cooler during the day, toasty at bath time, cooler again at night.
I would turn your rads up (on the thermostatic valves if fitted, else on the lock valves) until the room they are in seems to rise to a comfortable temperature when the boiler is on and heating the house IYSWIM. This might mean you want the rad in the bathroom up high (as they're often cold) but the rad in the master bedroom lower (as they're often warm, and you don't want to sweat buckets at night IYSWIM). Well, not unless you're with a man with an impressive six pack.
Sooooooo.... to answer your specific issue, you could leave your boiler on all the time and just twiddle the knob in the hall to set your comfort level as you go in and out, or through the day, else you could invest in a programmable stat, else you could do what you are presently doing and have the timer set so that for some of the day it's off, and for some of the night it's off, but other times things are set to whatever the hall 'stat is set on.
The choice, as they say, is yours.
hth