The core Symbolics SYSTEM system I see here is version 501.51. It consists of a bunch of other systems like SI, Embedding, L-Bin, Tables, Scheduler, Netboot, Common Lisp, SCT, Garbage Collector, Flavor, Error System, Language Tools, Network, Lisp Compiler, Bitblt, Fonts, FS, Bin, Time, TV, Presentation Substrate, CP, Dynamic Windows, Debugger, I Linker, Fep-FS, ...
I don't see much of that in System 99 from MIT.
Stuff like X11 and NFS is also not random stuff. Open Genera uses it for its console and its files.
> seeing that it doesn't really support CL very well anyway
Well enough that it is able to run a lot of its software written in Common Lisp. It's able to run stuff like PCL, ASDF, ITERATE, ...
System 99 is from 1984 (?), Symbolics started in 81/82. Open Genera appeared 1992/93. You are ignoring a full decade of development.
Earlier:
> Genera did a few cool things but in the grand scheme of things it is essentially not much (the Dynamic Listener probably being the most interesting thing, the rest of the system was essentially the same).
I would guess that less than 20% of the core SYSTEM is essentially the same (but often quite a bit enhanced). For the rest of the software, I would think it's even less. Which is not surprising, since System 99 did not support the 3600 systems, the G-Machines, the I-machines (XL400, XL1200, XL1201, UX400, UX1200, NXP1000, MacIvory 1/2/3, ...), Open Genera, ..., because all that was developed later by Symbolics.