Coving will flex better as it's fixed at both surfaces, so won't be an issue, and a small squirt of expanding foam will fill the gaps, and be fine.
Whoever did that pipework, should be hung drawn and quartered. I have no idea if it breaks any regs, but you've got a water source above an electrical system - and has anyone tried to unscrew the Magna clean yet - and what's the control unit above the flue pipe.
I'm at a loss as to how to suggest you cover that over, as you need access to it, so you can't use the coving. You can't box it in above the boiler, only above the window, and the mismatch is going to look odd.
You could get the pipework lowered, and then put a false box above, and then put the coving on the front of the box to make it look the sams as the rest of the room.