As far as which is more expensive, it's totally industry specific. Some of my clients pay a lot more on one or the other, and it really depends on the keywords involved.
Dont they use an average CTR to estimate and provide you with a price and position per click?
Have you been paying more or have you been paying less than what you have seen on the estimator after using it in real time?
The estimator prices on G are pretty worthless.
I have some that the estimated traffic and position are way off, both higher and lower
In many cases, some of those figures may appear a little off because there are other keyword combinations, possibly irrelevant to what you are bidding on, that others are bidding on, at a higher rate.
So, if you are bidding on "A" and "B", there may someone else bidding on "A" "B" and "C" at .90/click.
Because you're ad will show up for the terms "A" "B" and "C" the estimator will tell you that you need to bid above $0.90/click. Even though the lowest rate for "A" and "B" is $0.27, the estimator is being accurate in telling you that you need to bid above $0.90.
As an experiment, I looked at our broadest campaign. Google estimated the campaign price should be $50/day to maximize our bids. We put the spend cap at $50/day. After one week, we'd been number one the entire week, and spent a total of $135 with a nice ctr for that campaign.
It could be that the G estimator doesn't take into account negative keywords, and the impact that has on search totals.