No the update won't force exclusive use of the CyberSCSI (at least it did not do that on my A4000T). I ran both the A4091 on-board SCSI and the CyberSCSI together, no problems).
I don't know what limitations you will have without the INT 2 fix though.
Edit: I see what you are getting at now: it shouldn't make a difference whether the previous owner had it set up to use the SCSI module, because I had mine attached and then removed, and moved drives from one controller to the other, and all was fine. The CyberSCSI is optional, even afer you install it.