The open source vs proprietary decision is usually a decision taken based on exactly this difference.
The sole reason for many companies to upstream some of their stuff is that they do not have to keep up with the firehose of upstream changes on their own.
Some companies might be in the position to make that choice, but I'd guess most aren't really equipped for it. First of all there's the issue of getting your changes upstream, you have to convince the community it's worth their time to help maintain your code, plus a quality bar you have to meet. And then once it's upstream you're committed to drinking from the firehose, instead of updating at your own pace, and there's extra scrutiny on every change you make.
I really think most of these proprietary users are just figuring things out as they go, and doing that upstream 1. wouldn't be accepted, and 2. wouldn't make sense for them in the first place. But I'll admit that's speculation, I don't have intimate knowledge of what everyone's doing :)
Those are intentional deviations from the standard, and I think there's a reasonable assumption that those stay the same/compatible from version to version. I think the other kind are a bit more problematic, and without a standard it can be difficult to tell whether your assumptions are reasonable.
Well I don't think most people these days are interacting with assembly by hand-writing programs. The real users of ISAs now are compiler authors, and the simpler and regular languages seem better for them. So is there some other reason (other than inertia) that RISC isn't practical?
