Can I put the lid on during the boil?
This is not recommended on the Grainfather brewing units as it can cause a boil over.
It can also affect the flavour.
In wort, there are sulfur compounds that evolve and boil off at the start of the boil. If they aren't removed during the boil, they can form dimethyl sulfide which contributes a cooked cabbage or corn-like flavour to the beer.
If the cover is left on the boiler, or left on such that the condensate from the lid can drip back in, then these flavours will have a much greater chance of showing up in the finished beer.