A lot of these commands can produce spool files and/or output files, which you can FTP back to the "home" system for processing. The outfiles should all have a field for the system name, so you can differentiate systems.
For the commands that only output spool files, you'll need to copy the spool file to a physical file with a record length of 133 and use a HLL program to process it (I have also done that with good old Query/400, by defining the headers on the reports and excluding them, and sending the result to an outfile).
There may be API's to do what you want (I know about QWCRSVAL, which is the equivalent of RTVSYSVAL), you might want to see if you can use these API's in a CL or RPG program on the remote systems to get your data. Then, it's just a matter of getting all the info over to the "master" database.
It will be time consuming, also, to write this application, but it should be worth the effort. Good luck.
"When once you have tasted flight, you will forever walk the Earth with your eyes turned skyward, for here you have been, and there you will always long to return."
--Leonardo da Vinci