The VC4, which is well over 90% of the Silicon in the SoC is the Broadcom VC4 GPU. That is part of all Pis, so far, and one would expect that it--or a follow-on upgrade of it--will be in any new SoC used in any future Pi. The SoC *is* the "guts of the RPi 3". The only other major components that is on the CM3L is a 1GB RAM module. The CM3 adds 4GB of eMMC flash. The NEC version of the CM3 replaces the 4GB eMMC with 16GB of eMMC.
(Note: I am reading the question as referring to the CM3. The CM uses the original Model B/Model A/A+/B+/Pi0/Pi0W(H) SoC...single core ARMv11, 700MHz to 1GHz, 512MB RAM with 4GB eMMC added.)
Yes--though not on the CM3L. Also "different" (in this case does not necessarily mean "better".
Yes, and the I/O board can be customized. The development board (done by the RPT), exposes lots of GPIO connections as well as both camera and display interfaces, but only a single USB connector. On the other hand--to give an example--the WD SATA Adapter has two USB ports, no Ethernet connector, no GPIO pins, no DSI, no CSI, but it does have a SATA connector...and an actual power switch.2. Needs an IO board
The CM3 sells for less than a Pi3B, and the CM3L sells for less than the CM3. The development carrier board costs considerably more. The WD SATA Adapter is less than a Pi3B, but a CM3 (or CM3L) plus the SATA Adapter comes to more than a Pi3B.3. More expensive
The interface (the SODIMM-style edge connector) pinout is published. I don't know how that works with regards to your--or anyone else's--definition of "open source". The binary blob it takes to boot a CM/CM3/CM3L is the same closed source code that boots any other Pi.4. Open source (yay!)
How are you at circuit board design and surface mount soldering? Remember that you will be responsible for having the required power and power safety circuitry correct as well as an interfaces you want on the carrier board.
The power circuits are generally on the carrier board PCB.
You *really* need to get your hands on the RPF CMIO3 board so you can get a glimpse of what is involved. I trust that you are aware that it is quite common to have 4 or more layers with winging and ground planes in them.... Designing a modern PCB is a complex process and it's really a 3D structure. What the CM3 does is to take the hardest part of the design--putting that in the module--so that the carrier can be *comparatively*--but not absolutely--imple.
I'm sure Element 14 could do it through their custom Pi program. Of course, you'd have the up front expense of covering the engineering development charge and you have to commit to buying 3000 to 5000 of the boards once they've been made... Alternatively, if you can find a local maker space, there may well be people there who could help you get started and might have the equipment to make a one-off, fairly simple, carrier board...or know of companies that will make small (i.e. 10 or less) runs from your design. There is the minor problem that if your design doesn't fork for some reason (even the pros don't always get it right the first time...or the second), then you'll have to pay for another set with a revised design. Repeat as needed.
To get an idea of how hard it is, take a look at the public information (e.g. About and Forum pages) on the fiveninjas site.
As a concept or to go into a business? Once more, I can't emphasize enough that if you are interested in the CM, read the Compute Module forum. That's where the active CM discussions take place.