I'm glad that you were able to resolve this without having to redo the entire config.
I think you have some valid points but we have always suggested clicking on the yes to all button. The way the message is worded makes it seem like you would be overwriting existing files with older versions but this is not the case. These are files that should have different dates but you should not worry about overwriting them. Choosing 'yes to all' is the correct option.
As far as an order of product installation we do not have a list for this, like you noted you should try installing the latest extensions last, but the order should not make a difference. I have brought this up with the managers to ensure that they see the feedback.