Never had that experience. Most engineers I know will be conservative on that. I think if you come in lower than what it will actually cost, it really puts the developer in a bind because they are getting financing based on that amount. Did you guys add the contingency as well (btwn 10% and 25%)
Remember though, it is 'An Engineers Opinion of Probable Cost', not a cost estimate. (I suppose there is some legal interpretion between the two which is lost on me) I think what is more important is making sure you quantities are correct (Ie cut/fill, asphalt/concrete, sewer pipe, water, FH, etc)
Here is a hypothetical situation that someone told me once. Suppose you screw up your quantity estimate and did not count 1,000 feet of storm pipe. A savy contractor in business for 30 years sees your mistake but keeps his mouth shut.
On his bid, he lowballs everything except storm pipe, which he hyper-inflates. Overall his bid comes in low (gets the contract), but his unit cost for storm sewer is $500 per linear foot.
Then when the inevitable change order comes, he can point to his agreed upon bid amounts and make a killing....or so the story goes...wonder if that could happen.