The following convention seems to be broken:

If you explicitly specify a command line flag, you get ":=" instead of "=" in the -XX:+PrintFlagsFinal output:

For example,
    uintx MarkStackSize := 4194304 {product}

The ":=" is also set if the value has been ergonomically decided. From PrintFlagsFinal there is no way to find out whether the flag has been set on command line or via ergonomics.

Some GC argument processing code may not adhere to this, i.e. may set option values without influencing the output. There are a few bugs already filed for that:

JDK-8024137
JDK-8012591
JDK-8037283