Okay, so after MUCH thinking and deliberation I have decided that I will continue to release new versions of the '360 Modification Disc', however, the disc-based version will not have any advanced features in the future. Meaning that the disc-based version will continue to be updated as new firmware versions come out, but the features will remain the same. (the disc-based version will ONLY be able to automatically flash drives, nothing more)
My reasoning for this is that NTFS support in DOS with the disc-based version is not reliable enough to allow NTFS HDDs to be used as a medium for containing files that would be used with the advanced options the disc would have offered. (like the USB version currently offers)
NTFS support under DOS works just fine for backing up files, but I do not trust it beyond that. Therefore, the disc-based version will only offer the option to 'automatically flash' your 360 DVD drive and nothing more in the future. When new iXtreme firmware versions are released, the disc will be updated.
So, just to finalize and clear things up, the USB-based version will always be the 'better' option, and will continue to have features added to it, and will continue to be regularly updated. The disc-based version will also continue to be updated, but only when new iXtreme firmware is released, and will not offer any advanced features beyond automatically flashing drives.
I appreciate your understanding in this matter.