Amontillado wrote:

+ arrange RTF files in the order I want in Devonthink
+ click/shift click/command-C to copy the files (particularly their
names) to the clipboard
+ open the terminal app and go to an empty directory
+ run indexfiles (my Python script)

That feeds off the clipboard and copies the files out of Devonthink to
the empty directory, prepending an index number in front of each
filename. The Nisus "join files" macro will then see the files in the
order as presented in Devonthink instead of alphabetized based on
original file name.

Devonthink as Scrivener, complete with a compile feature.

Your process sounds a darn sight more "complex" than the three editor windows and compile in Scrivener.