What you have missed is that this was debated to a painful degree in the last few years. Since you were not a SB member then, you missed it all. I gave you a summary of how you can deal with this issue of deviation from standards, but you ignored it. I will try again.
PADI does not allow you to withhold certification from a student by adding additional requirements beyond those identified in the standards. They do not, however, prevent you from adding additional information to the course as you teach. I (and every instructor I know) adds information they feel is important. We don't put it on a final exam, but we can easily see by observation if the student understands. For example, I add information about gas planning, and I go more deeply into decompression theory. In the shop with which I was formerly associated, the Course Director polled all the instructors to find out what they were adding to the course. He then designed a common program that added all the "best hits" in presentations to the students in addition to the eLearning. PowerPoint presentations were created on some of it. No, there was no formal assessment, but it was obvious when students understood the content. This was done with the full knowledge and approval of PADI.
Next, a program like yours could easily make your instructional program a combination of courses. This would be similar to how schools like Harvard and Yale run graduate programs. (Or at least they used to.) It is a Ph.D program, with the Masters degree conferred only to those who for some reason did not complete the program, which rarely happens. You can combine OW and AOW, for example, and many programs do. You can also combine OW with specialties.
Speaking of specialties, you can pretty much do whatever you want here. Just make an outline and send it to PADI to have it approved as a distinctive specialty. I have one for Diver Planning that covers just about everything a recreational diver needs to know. Jim Wyatt and a couple other veteran cave instructors got a PADI Cave Diver certification approved--it has all the same rights and privileges of cave diving certifications from organizations like NSS-CDS and NACD. If they can get a full bore cave diving course approved, you can get any level of course approved. Thalassamania, who just joined this thread, teaches scientific diving. He could easily get his full certification program approved under the title Scientific Diver.
Finally, you can do workshops in addition to certification programs. these teach whatever you want to teach without the need for formal certification. I have just designed one that teaches skills similar to the GUE fundamentals course, and I will be offering it this spring in a PADI shop.