Alignment usually means setting up the oscillators so that the
frequency and wattage/modulation are correct. I believe the term comes
from the good old days, when radios had paper or metal cards marked
with the frequencies that had to be aligned mechanically with the dial
markers.

"Peaking and tuning" is not in itself a bad thing; there are a lot of
ways to do it, and not all of them are correct. Even if you are bending
the 4W carrier limit, you still want to make sure your modulation is
correct, and that you are on frequency, because this will make your
received signal stronger and clearer at any power level. I've seen
hacks tune radios up to 100W carriers without setting the modulation
correctly, resulting in a radio that transmits a very strong but nearly
silent signal for miles and miles.

The other possibility is that he's trying to get some extra bucks out
of you. I know the guy at the local CB shop here, and he aligns rigs
for free if you buy them from him.