so if the sata controler have an option rom, and the bios is compatible it will load the option rom during boot. The card will detect the drive. If the card doesn't detect the drive than you can't boot from it. From bios the option generally is called scsi, as boot to int13 card.
I shouldn't need to explain that you probably need to disable the onboard ide controllers to free up IRQs.
IF the bios loads the option rom it detects the drive than you can install dos to it. If the controller card is in IDE mode.... not raid mode. raid mode will not work unless you create a raid with 2 drives then through int13 it is detected as a single drive to dos. If your card has a IDE bios i suggest thats what you use. there are raid and ide bios for the controller card itself.
I can tell you strait up that 98 or me is not going to work on that card if its in raid mode. If you do ide mode you can use rloew sata patch maybe. http://lonecrusader.x10host.com/rloew/ptchsata.html
I don't see how cloverboot loader will help you. You maybe trying to use a nvme, but you are not using it as pci-express am i rite. You are using a adapter that is translating it in hardware somhow to sata or somthing else, so that is irrelevant. If the card doesn't see the drive during option rom detection than you cant use it.