I love abominations, that's all we have lately. Quite popular. My comments/observations:
I yell at EE's all the time: "The fuse comes first". You have it in the middle so there's no coverage for a short on +UNREG feed or U4 etc. Put the fuse first at DC IN+.
The water detect circuit is better done using a quad comparator like LM339 or
TS339 instead of TL074. (
LM339B is the revised part)
A single supply at 5V is all you need, you do not need to generate a -5V rail for it. Just need output pullup resistors. Then D10, D16, R24, R35, R8, R22, R26 can be deleted as well as the -5V circuit U1.
The water sensor circuit is not done right - it should have an input cap used so you get no DC leakage current at the electrode. If there is iron and copper or something making -0.4V it will corrode due to D15/D19 being on all the time.
Same for probe outputs, a 0.1uF cap is used there because your square wave is never perfect 50-50 duty cycle and corrosion happens. I'd add LED's to show each electrode Water_In_1,2 status.
The drive resistor for the BCP56 is a bit too high at 10k, I would lower it to 2.2-3.3k for more base drive.
You don't need such a big fat diodes SS24 across the relay coils even BAV99 is enough.
MAX6675 is sensitive to RF. A cellphone/WiFi etc. near the thermocouple wiring will cause crazy readings. So you need RF filtering on the input: ferrite beads, caps and dedicated 2-pin terminal block for the TC. I don't like the IC, I said more
here but did not try the newer MAX31856 although it looks equally awful (note: cannot ground TC).
'328PB already has a watchdog built in. Using the external one SP706, it does not (hardware) disable the heater/boiler relays if it trips so I don't think it's any safer. Also, it nuisance trips and gets in the way during programming, you need a resistor/jumper to disable it.
The heater/boiler already should have limit switches PLC safety control and not cause a bad happening if the demand for heat/boiler relay gets say stuck on due to a failure of this board.
I don't know what "phase chopping control" is. If it's mains AC phase control, don't you need AC zero-cross coming in to the MCU?
ENC_A,B usually have low value pullup resistors and caps for ESD but you have something for the switch- it seems odd.
You need lots of PCB copper heatsinking for the 5V reg especially with two LED displays and relay loads.
Not sure what DC_IN is for voltage but using say 12V relays powered from that will offload the 5V reg.