Answering my own question, thanks to an hint from @ktf, I found out that at least since 2.6.28 [1] there are IOCTLs (TCGETX, TCSETX, TCSETXF & TCSETXW) to setup extended attributes.
They seem to have been added to the upstream kernel on 13 Oct 2008 [2].
These extra IOCTLs (compatible with SYS5) allow to configure each of the extra pins handling individually.
See the link for the original RHEL patch [3] and look on the attached test case for an example of how to use it.
The IOCTL definitions are on the "asm-generic/ioctls.h" file and the structure and flag constants are defined on "linux/termios.h" (in "/usr/include", off course).
UPDATE
Further research shows that the generic serial support for this IOCTL wasn't merged into the upstream kernel source. RHEL 5.3 has it, but not the upstream 3.0.6 kernel.
That means the ioctl() call will fail for any other kernel that didn't port the RHEL patch [4].
[1] http://lxr.free-electrons.com/ident?v=2.6.28;i=TCGETX
[2] https://lkml.org/lkml/2008/10/13/120
[3] https://bugzilla.redhat.com/show_bug.cgi?id=445211
[4] https://bugzilla.redhat.com/attachment.cgi?id=315300&action=diff