This really is about the new Global Dossier (and PAIR Modernization seemed the closest category to comment in). Specifically, in the new Citation List Beta release, the field to accept application serial numbers is limited to 8 characters, so if you cut and past an application serial number in the format: XX/123,456 the end result will be XX/123,4 with the last two digits truncated (similarly, XX/123456 will be truncated to XX/12345).
It makes no sense and is much more burdensome on end users to be forced to hand type in serial numbers and not be able to cut and paste the serial numbers unless they are in the form XX123456.
I note that the USPTO PAIR system displays serial numbers in the form XX/123,456, so you cannot even cut and paste between these two USPTO systems.
In short, all USPTO systems should accept numbers in all commonly used formats, if not in all formats.