While I understand the logic of checking for Barracuda and large prefixes during the installation, I'm not so convinced about checking for innodb_file_per_table during installation.
For smaller installs, being set either way is not particularly problematic, since if not enabled, tables may be dropped and the space not immediately reclaimed by the filesystem, the space is still usable by MySQL.
The problem comes in for us with larger installations when using AWS and Azure, namely that replication of databases on these environments works much better on having one large tablespace that all tables are part of, and performance is improved as well in our experience.
I'd argue that this is also a decision that systems administrators should be making rather than applications; it should be transparent to the application whether it's on or off, and trying to impose logic for one set of users in the application to the detriment of others may not be ideal.
For now we've simply resorted to manually removing that test during installation but it really shouldn't be application-level.