"It is Earth's atmosphere not its magnetic field which does most of the protection against high energy particles that punch easily through our magnetic field."

Without the earth's magnetosphere, the crew couldn't survive in ISS- solar flares would kill them & Galactic radiation would probably adversely effect them over long term stays. But are you right in that the high energy particles that get through Earth's magnetosphere are mostly blocked by our atmosphere. Though there are high energy particles which get through our atmosphere- and hence the need to put some observatories beneath a mile or so of sheilding [underground]:

"Most neutrino experiments must address the flux of cosmic rays that bombard the earth's surface. The higher energy (>50 MeV or so) neutrino experiments often cover or surround the primary detector with a "veto" detector which reveals when a cosmic ray passes into the primary detector, allowing the corresponding activity in the primary detector to be ignored ("vetoed"). For lower energy experiments, the cosmic rays are not directly the problem. Instead, the spallation neutrons and radioisotopes produced by the cosmic rays may mimic the desired physics signals. For these experiments, the solution is to locate the detector deep underground so that the earth above can reduce the cosmic ray rate to tolerable levels."
http://en.wikipedia.org/wiki/Neutrino

"I'm not sure what the wave of probes since the late 90's have indicated, but earlier estimates indicated Mars could have enough volatiles to produce about 2 atmospheres of pressure if warmed up. With a lower gravity thats over 4 times as much mass over your head."

Well, there are plenty of oxides [40% of the Moon's mass is oxygen- and this also true of Mars]. But there isn't enough CO2- there is much more H2O than CO2 on Mars.
To get a idea, if you froze out Earth's atmosphere, you would get globally about 20' of liquid nitrogen and 10 feet of liquid oxygen [and inches of H20 and argon]. So you taking about 120' ft globally of some violatiles.