The old thread has been closed already, but I just found a way to solve that problem of concatenating multiple config files from separate directories in rclone.
Sadly it only works for zsh. After dabbling recently with zsh's slightly lesser known feature of process substitution (which instead of pipes uses temporary files) (which was really useful when using files without extensions), it struck me that this could be used as well for rclone.
Here it is: rclone copy <REMOTE1>: <REMOTE2>: --config =(cat .config/rclone/<REMOTE1>.conf <(gpg -d <REMOTE2-ENCRYPTED>.conf))
works like a charm It was especially useful when you have encrypted .conf files like in the <REMOTE2> example above. I couldn't however decrypt the .conf file on the command line if it was encrypted with rclone's config, so I went back to standard gpg.
Using regular shell process substitution results in error (that's why it's a zsh-exclusive for now): Failed to load config file "/proc/self/fd/14": seek /proc/self/fd/14: illegal seek
I hope that it will be useful for others as well. This simplified my usage of rclone by like a lot.
PS did you know that you can use cat command to combine files
PPS do you mind if I tag you @asdffdsa - I thought that you might find it interesting - maybe you could unlock the previous thread to update it with this suggestion?
I am not exactly sure why combining conf files is a good idea.
I have not used the rclone.conf file for many years.
Here is my setup of conf files for Gdrive
I have a single file called drives.conf
This single conf file has all the information for every TD I have access to. It is literally only meant to inspect drives so I can se contents quickly by using 1 conf. But it can also handle moving stuff from drive to drive as there are no limits on moving stuff from TD to TD
I have another 3,000 conf files 1 for every TD I have access to.
I have 200,000 SA accounts, this means I can auto cycle them via cmd without having to cycle through a small number of them.
This was done because even as a Workspace owner Google did terminate some of my SA, but now with so many I cycle through them all before going back to SA 0 which means it takes a long time to cycle through all the SA accounts.
NOTE: I never use tools like gclone etc, I find they can easily create duplicate folders when there is an error. So I am strict on using rclone commands directly to prevent this form happening
Since I use SA for everything this means I even used excel to auto generate my rclone config files.
Some friends have access to some TD they shared with me. To do that they simply copied their rclone.conf info for that TD and I pasted into. The token I get rclone auto updates it every time I run it and their token and mine never match yet I still maintain access to the token/TD.
I use excel to even generate all of my rclone commands for 3 reasons
It is easier and faster then simply manually typing it out
I can make a spreadsheet designed for a specific remote upload and assign it as many SA accounts
required to upload it
I have a track record of every file/folder/domain etc I have ever used rclone for
I will modify my excel spreadsheets and post them in the Howto Guides for others to use
It depends on use case, I guess that for most people it won't be useful, but in this case one of the config files was encrypted and ideally its decryption happened only within the "scope" of copying/moving/deleting files between these remotes. But it's probably an edge case.
It was especially useful when you have encrypted 
