Do they issue/hold walk-in permits for those that want to hike Onion Valley to Whitney Portal, or do you need to get the Trail Crest permit through recreation.gov?
Yes, through Rec.gov.
I have never had any problem getting one or two walk-ins so long as I walk-in on a Weds or Thurs.
Also I've done the HST and JMT and I preferred the JMT approach from Kearsarge. I hear the Siberian Outpost is pretty dry, sandy and miserable (the section of PCT as it wraps around the west face of Cirque Peak)
See here:
http://www.sierradescents.com/hiking/pacific-crest-trail/2008/onion-to-cottonwood-10.html
