The InnoDB internal tables SYS_TABLESPACES and SYS_DATAFILES as well as the INFORMATION_SCHEMA views INNODB_SYS_TABLESPACES and INNODB_SYS_DATAFILES were introduced in MySQL 5.6 for no good reason when the InnoDB support for the DATA DIRECTORY table attribute was introduced. The file system should be the authoritative source of information on data files. Storing information about file system paths in the file system (symlinks, or even the .isl files that were unfortunately chosen as the solution) is sufficient. If information is additionally stored in some hidden tables inside the InnoDB system tablespace, everything unnecessarily becomes more complicated, because more copies of data mean more opportunity for the copies to be out of sync, and because modifying the data in the system tablespace in the desired way might not be possible at all without modifying the InnoDB source code. So, the copy in the system tablespace basically is a redundant, non-authoritative source of information.
For compatibility with older versions, we might want to preserve the INFORMATION_SCHEMA views, but make them reflect the fil_system cache.