Thanks nanofrog - I was under the impression that setting up a raid merely stopped installation of windows - but would not render an existing windows installation unbootable...are you 100% about that?
I have read some of your very informative posts on the issue, but I have also read some things which seem to directly conflict with them (please see
https://forums.macrumors.com/archive/index.php/t-690256.html) and as I want to do this myself (raid & windows) it would be great to get some definitive answers to a few questions...
If you start with a "blank" system (add in the drives for RAID physically, load the OS disks to create the array, then install the OS), and then install a separate disk for Windows/Linux, Yes.
If you notice, the methodology in the linked thread is different. The OEM drive was BC'd with a both OS X and Windows. Then the array was created,.... Now consider it's the only post like that I've seen, as well as the end result of having 2x OS X installations. BTW, there's no system information given (actual model of MP, as others can actually boot Windows off of the ODD_SATA ports; just not the 2008 systems).
I don't consider having to perform a second OS installation to make it work acceptable. Not over the wasted capacity (HDD's can be had relatively cheap), but in terms of time (not just to do it the first time, but what may be needed later to fix problems/keep things running) and unknown stability (both are intertwined, as instability = much more time needed to get it running again).
So for a simple and fully functional answer, using a separate disk for Windows via it's own controller card is the best way to go about it. It's easy, won't require substantial amounts of time if there's a problem with Windows (beyond what would normally be required for the particular issue), and isn't that expensive. It operates the same no matter the order you go about it (start with OS X array, or do the card + disk for Windows first, then OS X array).
No hacks involved means safer (stability), and if one OS goes down for whatever reason, you've an other OS that's functional (allows you to boot into it for diagnostics or internet access to find a solution; particularly useful for those that don't have a second system on hand to use for such purposes).
So when I see such questions, I keep it simple.
1. Is it possible to boot windows from an odd SATA Port? (I know you can't install windows onto an odd sata port drive, but the post I linked to above suggests that if you install it elsewhere, you can then move it to odd sata and boot)
Unfortunately, not on a 2008 system (others indicate it does work on '06, '07, and '09systems, and it should be the case on the '10's as well).
I worked with someone over the phone with that methodology on a 2008 system, and it didn't work (I use hardware RAID controllers, and it wasn't an issue).

One of the downsides of getting the first EFI64 MP produced I guess.
2. Does creating a Raid actually change the firmware forever?
No, it's not permanent. Disk Utility will change the firmware setting if you delete the array (not talking about data, but the set - end result = individual disks again).
3. Do you definitely need a separate SATA card to boot windows if you have a raid installed? Again, the post I linked to suggests you can boot windows with a raid installed (albeit in this example, he says he is booting windows from the odd SATA while the raid is on the 4 main bays.
See above info.
4. If the separate SATA card is required, can that SATA card you linked to be used to for a mac HFS+ partition as well (currently I have my windows as a partition on a disk with a mac partition on it too, but the mac partition is not my OSX, it is just file storage)
Yes.
Silicon Image, and other vendors that sell cards using that chip have OS X drivers. But some have had difficulties with what drivers will/won't work (unknown card source), and had to experiment to find ones that would. There may have been an occasion or two that they may not have been able to find drivers that worked for them as well (not sure here, as they may have given up before trying all available driver sources).
I have a windows partition in another drive and use an EFI boot tool (rEFIt) that picks up all the different partitions and gives me a boot menu, so I'm not worried about that. What I don't have clear is the process of backup then restore once the raid is created...
Then experiment around with a spare disk before creating the array (i.e. larger drive), or do it manually (find your files, and store on a separate disk, USB stick, ....).
I don't use TimeMachine myself, as I don't use OS X (use Win7-64 & Acronis for backup and cloning - it works well for me, and I need to be in Windows to get stuff done). But I recall others stating TM can be used without it creating partitions on the destination.