Oh, I understand. You want to choose only some of the settings from various pp3 files on top of your .RAF.pp3 file.
To do that, after opening the RAW file with last saved profile, you CTRL+click the folder icon next to the drop down arrow in the Processing Profiles tab. (If you hover your mouse on that folder icon, you should get this tip) It allows you to choose which pp3 file to load and exactly which modules from the chosen ones to use to overwrite the current profile.
I think you already have what you’re looking for. The pp3 with the name of the raw file contains the latest work with that raw. The pp3 with the name of the output file keeps the work to reproduce that exact output file.
It’s possible to have as many pp3 files as you want, but as you have discovered, and as @RawConvert has pointed out, treat raf.pp3 as a temporary working file. There are load and save buttons in the processing profiles section.
When saving foo.raw to JPEG, RT saves foo.raw.pp3 alongside foo.raw,
and if “Save processing parameters with image” is ticked it saves another foo.jpg.pp3 alongside foo.jpg for convenience.
When opening foo.raw, RT auto-loads foo.raw.pp3 if it exists, or it looks for a PP3 in the cache, or if neither is found it uses default values.
As @james told you, you can save the actual state of your edit in a pp3 file. By “actual state”, I mean that you can select an entry in the History, or a Snapshot, then click on the Save button in the Profile Selector to store a complete pp3 file corresponding to this actual state.
Alternatively, if you reopen an image to edit it again, then load a pp3 file, you have to select the first entry in the History before closing the Edit tab (or switching to another image) if you want to ignore the “second edit”.