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I always look at it as two companies agreeing on the terms of a contract, no question is off the table. If reasonable questions are asked on both sides of the table there should be no reason to find hidden meaning or like/dislike the comments. I find it better to be honest and up front about my expectations as much as the company is theirs.

You "may" choose not to purse the job further (or they may choose not to speak to you again), but at least you have said your piece and it is better for everyone to find out it wasn't a fit in the beginning versus 2 years down the road.