You only need to remove all ammunition from your sidearm and magazine* as you travel through Portland. Once you cross over into Gresham, you're back among the sane and free population of Oregon. Even in Portland there is no requirement to case your sidearm for transport. In fact, it's probably a good idea not to as Oregon's definition of 'concealed' does not include any exceptions for firearms transported in a case.
*Portland's loaded magazine prohibition is arguably in violation of state law, but it's up to the individual if they want to risk/fight that.