You're thinking that "expenses" is the antecedent of both pronouns. It isn't.
"As it is" is an idiomatic phrase. It can go at the beginning of the sentence: "As it is, clients resent...". It is a way of stressing just how bad something is: the first part of the sentence is quite bad, the second part is worse.
"We can't pay our bills as it is [that's bad enough], but now we have to pay more taxes as well [that makes things even worse]."
In (2), the antecedent is not expenses, but the ten percent, which is singular. There are the fee and expenses, but on top of those (i.e., added to those) is another 10%. It is this 10% -- the 10% which goes on top of the other things -- which acts as a significant deterrent. The phrase "on top of the fee and expenses" simply describes which 10% we're talking about.