Do all of the Abbey Wood branch stations have platforms long enough for 11 car trains? According to Wikipedia Canary Wharf does, but I wasn't sure about the others. Maybe they could run only on that branch?
When we talk about the Core this is usually taken to mean all the 'new' stations from Paddington Crossrail through to Whitechapel and then on to Abbey Wood, as this part of Crossrail is entirely self-contained and separate from other railways with entirely brand new stations. I don't have a source for whether the surface stations (Custom House and Abbey Wood) are actually built for 11 cars, but as brand new Crossrail stations they'll almost certainly have passive provision for an easy extension if not.
Agreed that it does seem theoretically possible to run the Abbey Wood branch with 11 car trains that turn at Paddington while keeping everything else at 9.
Indeed I read a comment at London Reconnections that indicated the NR platform extensions on the GWML branch were all being built for 9, with passive provision to go to 11, so maybe Reading trains could eventually be 11 too. Not sure about Shenfield.
Disadvantage of doing this seems like it could cause loss of operational flexibility to have half your stock banned from a particular branch, and maybe some passenger confusion if trains arrive that are shorter than the platform edge doors would suggest, but crush loading during peak hours may necessitate it eventually.