It's usually slower to boot from an pci-e drive than it is from a sata 3 drive. You could leave windows on your sata drive and install all your programs on the pci-e drive. This is what I would do if I had that type of drive.
Yes, there's, a pci-e drive adds at least a 5 seconds delay before it's starts booting. The problem is that the uefi boot manager has to load a pci-e boot driver before it can start booting the computer.
I still walk about with a 256mb thumb drive. They kids here at work all carry terabyte external drives with them. They get really annoyed with me when I ask them why anybody needs that much pron. One of them has his computer at home hooked up to his giant hi-def tv. He nearly upchucked when I asked if he could make out the hairs on the pimples of a chick's ***. I love messing with them. It's sooooo easy.