Not necessarily. Well, maybe it does if you are using Windows but I should think not.
When the computer boots up it'll assign labels to the hard drives based on which SATA port they are plugged into, those labels will always be the same so that your MBR will always look at the right spot for where to boot up an OS. Easy way to explain is to look at my setup on which I am running linux. I have three SATA drives plugged into SATA1, 2, and 3. They get assigned sda, sdb, and sdc respectively. My MBR looks for the boot kernel on 1 of those 3 drives. If I went into my computer and swapped that one with another one it wouldn't know how to boot. Not too big of a deal since you won't often be swapping around your SATA cables. One issue that comes up is if you happen to plug in a new IDE device. Depending on your BIOS it may load up IDE before SATA (or maybe not) and thus bump your drives all up by one (new IDE=sda, old sda=sdb, old sdb=sdc, old sdc=sdd)
If you had a drive hooked up to SATA4 from the get go, when you booted from a Windows disc to install it should detect the drive and install it to the right place (along with the correctly configured MBR) so it shouldn't have to be on the first port.
As for the RAID, since it is mirrored your MBR can point to the correct spot on any of the identical partitions in order to boot so it shouldn't matter. As long as it is pointing to the correct drive in the first place. I have a RAID setup between SATA 1 and 2 (sda and sdb) on which I have two small mirror partitions holding my kernel, so I could set my bootloader to boot from either of them and nothing would change.
Marc