First, I had an older but great machine with a pair of 80 GB drives on it I used as a dual boot machine. I had Windows 2000 Pro on one Drive and Suse Linux 9.3 on the other drive. I installed Windows 2000 then installed Suse Linux and let the Grub Boot Loader in Linux come up on boot and offer booting into Windows or Linux. That worked just fine using the Linux boot loader at startup. You can't configure like that?
Next, yes a switch could be configured to swap the master / slave jumper setting but there is a much bigger problem which is why it won't work. Your PATA cable has the master at the end of the cable and the slave at cable midpoint. The IDE port is configured to see things that way. The Master is always at the end of the flat ribbon cable and the Slave is at midpoint. Therefore if you were to switch the drive locations by simulating changing jumper positions using a switch it wouldn't work. Can a switch be configured to replace the jumpers? Yes! Will it work for what you want to do? Nope, I doubt it.
I may be wrong on this, as I found something:
The IDE interface requires only one cable. All pins straight from 1 to 1, 2 to 2 and so on. The drives can be connected in any order. Only remember that one should be jumpered as Master and the other as Slave. If only one drive is used, jumper it as Single (if such a mode exists, or most common Master else).
Now if that is true as I read it than a master could be placed anywhere on the cable and likewise the slave.
Assuming I am wrong then you could do as you mention. Each drive would have 4 wires so either the master or slave positions could be made on each drive.