I know this thread is dead, but just for reference in case you or someone else in the future are curious... Sure they can! No auditor is going to look at this situation and say, "Wait a minute, you took a deduction
lower than you could have? That's a penalty" so it's generally not a problem. If you do the opposite (book a cheaper flight and then expense a more expensive one), that's definitely a big problem and also probably illegal.
However, if your company has strict policies about receipts and expense amounts you can always do the slightly shady "book two, cancel one" move - book one seat at the cheapest rate and another that's actually comfortable, print the receipt for the cheaper one, then cancel it within 24 hours to get a refund. I don't recommend this of course, but it is a way to get around excessive red tape.