Our shop is still clinging the EPS file. I have tried to get them to consider PDF's more often, but because of problems that our RIP software (ONYX) had with PDF's years ago, they've remained suspecious. It's hard to teach an old dog new tricks, especially if they've been burned. They also are clinging to the notion that CMYK is the best way to design something. Sigh. Luckily, most of our files come from agencies and we just need to create print ready files from an InDesign file, with all of the assets and fonts included... most of the time....
Remaining suspicious is understandable! My lead prepress tech is the same. We use pdf's...BUT we know exactly what works and what doesn't on the prepress end. We meticulously comb through art omitting any extraneous bs...like empy clipping masks...vector data off the artboard...
If you're running a good profile, the cmyk/rgb images should be nearly identical. RGB just saves space. I'm an imaging nerd, so I subscribe to the fact, like you, that the largest colorspace should be used right down to the file rip stage. If you have solid prepress standards and leave your rip alone as far as settings it works great.
CMYK should be used if you are working in Illustrator, however I prefer a spot color workflow when at all possible.
The problem with RGB in Illustrator is your grays...they go to arbitrary values dependent on your working space, which is bad.
I like Illustrator cmyk with RGB images placed. You get the best of both worlds.
The only real issue I've had with ONYX is certain blending modes not rendering. Same with Caldera. (we only really trust multiply)
We run Caldera...although I've always kind of preferred ONYX. The reality is, they are both VERY capable packages now, and make profiling super easy.
They can handle damn near anything you throw at them. I did a test the other day and sent a pdf test file with live stroke width effects active, and arrowheads with dashed lines applied. I just wanted to see what would happen, and it all rendered fine. I was blown away!