Because the whole point of this forced update was to funnel users through their partner for USPS shipping, not to improve the user experience.  

You will have to link stamps.com directly, but then you will always get double quoted USPS rates with no easy way to differentiate between which ones come from the ShipEngine USPS account and which ones come from your stamps.com account.  

Just make sure to NEVER fund the ShipEngine USPS account and you'll be able to differentiate which account you're shipping under by checking the "Current Balance:" field (zero for ShipEngine account, >0 for your stamps account).