For individual adventures, particularly those that leave the area of Shadow's Edge entirely, I would say the DM running the adventure can introduce any particular house rules or ban/reintroduce particular material if they wanted. Most players aren't going to mind tweaking their builds if they're particularly interested in a given adventure and once the adventure is over, they can come back to the fold with a few more tweaks.
Overall, we would probably want to keep house rules to a minimum within the general setting and area to provide a base line for DMs and players. When I'm running CO oriented games, I typically follow that course as a rule of thumb. The type of house rules that I do use for my standard games are listed
here. The biggest impact any of the actual changes (versus new content) have is probably the restriction on metamagic cost substitution.
That said, given that 3.5 is no longer supported, it could be interesting down the road to maintain some enhancements to older material to bring it in line with the final elements of 3.5. (Or potentially new content.) In my regular games, I have integrated a lot of Tome of Battle into older material that otherwise wouldn't be used for instance.
If something like that was done, a DM council (and possibly some of the more knowledgeable CO members to review if they were interested) would be required to maintain balance.