A partition on an MBR disk cannot be more that 2TB. To create partitions above 2TB you need to set the disk to GPT but then it will not boot (unless you have an EFI based computer rather than a BIOS based one!)
So even if you were able to create a bootable RAID >2TB you would have to partition it into partitions no greater than 2TB in order to boot it! So whatever you do you are going to end up splitting the disk into two logical paritions.
So the workaround in your case would be to create two RAID arrays on the disks. In my case, I created a RAID 1+0 array of 100GB for booting, and then used the rest of disks for a RAID5 array.
In which case what I suggest you do is the following (I'm assuming that you have no data stored on the drives or have a backup of any data on them).
a) reset the disks to non-RAID
b) create a new RAID5 volume on all 4 disks but when asked for the size enter 200GB
c) create a second RAID5 volume on the 4 disks but this time when asked for the size accept the maximum
d) Install the OS on the 200GB volume (which will be bootable).
e) partition the second volume as you wish.
After having the drive configuration set to RAID in the BIOS, I then made sure my boot order was set to normal so that the CDrom would get recognized first for installing to the first of two RAID volumes created. Specifically, I have the DG45ID motherboard with the latest BIOS as of this date with the G45 chipset and ICH10R raid controller in an HTPC get-up. There are 4 identical Hitachi 2TB 7200rpm Deskstar SATA drives set with a two volume RAID array. The first volume for the operating system I set to RAID 5 at the max I was able to set the volume to: 2047GB (2048GB and above made the array non-bootable). The second volume (as it will not let you create more than two volumes in an ICH10R raid array) I created a RAID 0 for the remaining space (scratch volume) and it read back as being non-bootable after volume creation. As the others have stated, there is no option that the user interface allows to select bootable capability or not. It is done automatically for you based on the size of the raid volume, be it in a single volume array or two volume array as is the case for this ICH10R chipset.