Why using innodb_file_per_table?
I don't think it's a matter of performance but of management.

With separate file per table, you can store different databases in different storage devices for example. 

You can deal with the case of very large databases in file systems that can't handle big files (at least postpone the problem until one table reaches the file size limit). 

You don't have uncontrolled tablespace growth. If you have some big tables that you drop, the ibdata file stays small.

One aspect that may have some effect on performance is the fragmentation of table data and indexes, which will be limited per table. But that needs testing to be confirmed.