This could be my ignorance of how mods interact, but I have Bob's and Angel's mods loaded up, and I get a message when I create a game that Thorium ore is not configured in RSO and will not be spawned. I can see that support for thorium was added in the changelogs for the mod. What am I missing? Thanks!

I'm not sure tbh.
I'll check - AFAIK thorium is not used for now and even if it spawns you won't have any use for it.
I'm assuming you enabled the ore by hand in settings?
Also make sure you have latest version of RSO. It seems to spawn for me when forced through settings correctly. But I have only Bob's mod set no Angel's atm.

Angel's Inf. Ore doesn't disable the auto-place for thorium-ore like it does to the other ores. It is not needed if you have Angel's. You can disable the setting for thorium ore in the bobs ore settings and it won't show up.

I am receiving this error message as well, Factorio v0.15.34 build 30875 win64 steam, RSO v3.4.5, BobsOres v0.15.6, AngelsInfiniteOres v0.7.1.

I don't understand what HellWatcher is attempting to say, above, or how to use that advice.

You can ignore the message if you have Angels Infinite Ores and you have Jivolite etc as ores. Thorium is unused and is not integrated by Angel so it's still enabled but bob's config is suppresed by angels.
As for advice above thorium is enabled in bob's ores settings in startup tab - you can disable it there.

Is there any way to force a heavily modded AngelBob / RSO install to disable Angel's Infinite Ores within the startup area?

There is a setting for that in mod settings for RSO. And it should be disabled by default.