Welcome! This forum has a treasure trove of great info – Scouters helping Scouters! Just a heads up, though - all content, information, and opinions shared on this forum are those of the author, not the BSA.
Yes the council can still register them as a Cub Scout. We had a lot of these last year that were already 11 in 5th grade and had to use paper applications. I had not heard of any this year, and we registered over 800 new cub scouts in our district, so I was hoping they had fixed this. Very sad that they have not, but surprised we did not run into any.