Maybe I don't understand your question but I'm not sure why you feel that having reporting marks from fallen flags would be confusing. The railroads and its employees view reporting marks as just some letters and numbers. We could care less about whether a car says ATSF 12345 or BNSF 12345. I think you're tying a railroad name to a reporting mark as in "ATSF=Santa Fe" but it isn't necessary for a railroad worker to understand what "ATSF" means.
Also to clarify why the railroads cannot add additional digits to the car numbers, railroad car reporting/computer systems are only designed to understand up to 4 digits for locomotives and up to 6 six digits for freight cars. This is why after the Union Pacific acquisition of the Southern Pacific that UP created a new reporting mark for it's yard locomotives (UPY) because they wanted to keep certain locomotives in specific number ranges and there wasn't enough numbers available with the 4 digit limitation.