The pipeline editor creates only processing scripts that are chained. The output of the first process is the input to the second one, etc:
https://neuroimage.usc.edu/brainstorm/Tutorials/PipelineEditor#Selecting_processes
If you select only one channel in the first process (eg. A1), the second process receives one file only in input: the channel A1 extracted for all the files you had initially in your Process1 list. The requested selection of a second sensor (G16) fails (and probably returned a warning or an error), and returns all the data in input.
If you want your script to behave differently: generate the corresponding Matlab script, and for all the processes, use the initial sFiles variable, and get the output of the various extraction processes in variables named in different variables (eg. sFilesA1, sFilesG16...)
https://neuroimage.usc.edu/brainstorm/Tutorials/PipelineEditor#Selecting_processes
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting