I think that PIO transfers only have to be done with interrupts disabled on really old, evil controllers (without unmask set). I don't think libata ever disables interrupts during transfers(?)
That's what "hdparm -u1" (or -u0) controls.
But it doesn't matter a whit here. The problem is that the IDE interrupt
handling can take a long time, regardless of whether it unmasks IRQs or not.
And if that IDE interrupt interrupts a serial interrupt, then the serial
stuff won't get handled until the IDE stuff completes. Thus the problem.
The "fix" could be to have the serial IRQ handler never unmask interrupts,
but that's a bit unsociable to others. The IDE stuff really needs to not
do so much during the actual IRQ handler.
Ingo's RT patches would probably fix all of this.