Way back in early W98 days, I used to call on whichever drive I wanted during start up. It had the unanticipated and extraordinary characteristic of allowing one to see into the dead drive. So, it wasn't as dead as the setup seemed to imply. Furthermore, one could write files to that second drive.
Interesting, I think I know what you mean, I have a system that used to have a little quirk, namely that the primary hard disk would sometimes fail to spin up in time to be recognised by the BIOS, so the secondary disk would become the boot disk (as it had, in fact, a complete Win 98 installation).
So in fact I had (sometimes and unpredictably) the ability to boot into Win98SE even though the primary disk was Win2K - however, the WIN2K disk remained off-line until the PC was rebooted (and would have been invisible to WIN98 anyway, as it was NTFS).
Now I'm not saying you are wrong, but I have never heard of any BIOS on a PC that would allow a choice of disk to be marked active at boot time! Yes, the boot order can prioritise FDD, CD, HDD and network, but I've never seen a boot order with primary and secondary HDD options.
I am aware that it is straightforward to mark a disk as disabled / not present in the BIOS, allowing you to select the disk to boot from, but that means it would not be possible to access that disk until the BIOS was reset - by definition re-booting the PC.
The best you can get would be to boot disk 1 and be able to access disk 2 in that session, or just have disk 2 available.
SD