The
BAS Tonal/Tango patch 2 uses a self-extracting archive that also has some SFX scripting in it which starts a PBO patch tool.
This patch tool (PboPatch.exe) then allows the user to select the addon files that should be patched and subsequently does just that, i.e unpacks them and applies the new files and re-recrates the now patched addon.
It's not completely automatic, since it requires the user to navigate and manually select each addon that is to be patched. (There might be a way to work around that and make it fully automatic but I can't been a**ed to try to do it now)
Limitations of PboPatchOnly one: it can't unpack compressed PBO files (i.e addons that are packed with say MakePBO), only uncompressed ones (PBOTool). A lot of addons out there are compressed so this might limit its use for your purposes.
If I were you, I'd take a look at that and
- See if it's applicable to your problem.
- Figure out its usage and function (can be done by studying the Tonal patch 2 above)
- Start learning about SFX scripts in self-extracting zip archives.
- Armed with this knowledge, figure out how to make your own patcher/installer.
Good luck!