I suspect Holden service may get some kickbacks as part of their franchise agreement with Holden that put the 3rd parties service businesses at a disadvantage.
Nope, can confirm it's exactly the same price for dealers as third parties. There are plenty of back end shenanigans money wise but dealers pay a yearly subscription fee for SI/GDS/programming access. The shenanigans are for all sorts of other things, i.e. mandatory rental car program, customer satisfaction incentives/kickbackes etc.
There is a PDF version of the workshop manual floating around on here, I don't have access to SI anymore as I'm not at a dealer but the PDF copy is essentially screenshot extracts of the online version and 100% the same.
They COULD have allowed more freedom on them but it's always a trade off, particularly when using the same part across a number of vehicles. For example the body control module is the same part across a bunch of different cars, so it doesn't come preconfigured with any software - you have to install the module then connect to the GM servers and download the correct package for a VIN. The online system also ensures that when you replace a particular module, by making you connect online and download it, you have the latest software version for bug fixes. Older vehicles (i.e. the VE platform) had some "dumb" modules that came preconfigured with software ready to go, but when the software was updated for some sort of bug it makes the existing stock basically worthless (a good example of this is the HVAC control modules, they had software part number supercessions as well as hardware revisions).
The current setup is essentially the best tradeoff for all these factors, and while GM don't HAVE to make it available to everyone, they choose to (at a reasonable price I reckon too, excluding the MDI tool).