This is the way the PSD Import filter was designed to function. The new channel is dynamically generated by the PSD Import XT to represent the accumulated alpha of the current layer stack. The channel is updated every time the user changes visibility of a layer in the PSD. Alpha Mask 1 maintains the opacity of every layer in PSD file.
When you desire to output a PSD file that contains spot color information in addition to the CMYK channels, you must use Alpha Mask 1 as your choice in the Mask drop-down menu of the Measurements palette.In addition, you need to choose either Composite CMYK and Spot or As Is for your Output Setup. When you make these selections, all used spot colors are output correctly along with the process colors.
Note: If you select None in the Mask drop-down menu in the Measurements palette, all used spot color information is converted to process color. I you to apply spot color as a channel, spot color information will be hidden, and it will be applied as a normal alpha channel mask, i.e., it will not contain any spot color information.