In the end, you have to like the windows more than anything else since they are going to be around much longer than any contractor; so that should be the most important decision, and the installation shouldn’t vary much from contractor to contractor.
Remove all the variables from the equation that you can by selecting which windows you want and then ask each contractor to bid on the revised requirements. Much of the variability will be in the markup of the various windows, ask for info on how much they are marking them up too.
Whenever I do any work for anyone, I provide all receipts for the material to them as proof of the material costs. The only variable is how much I charge for the labor….and I’ve never had a single dissatisfied customer.