There is, of course, a reason for that, but it is unimportant now, because it disappears in the ratio of potential energies. But if you must know, look up the potential energy of a system of charges. If still unclear, come back.
Well, yes, but. The purpose here is to obtain ##U_2## as ##fU_1##, where ##f## is some factor. So we want to keep ##\sigma_1## inside the integral. That implies that ##f## will contain ##\sigma_1## and ##\sigma_2##, as shown in the message you quoted.
We have a region ##\Delta_1## and a region ##\Delta_2##. We can have a function ##g: \Delta_1 \to \Delta_2##. Now, because the regions are very similar, we can find a ##g## that is linear.