The queue is a simple csv file
| as column seperator. You could write a script to generate this file
Here is an example with 2 images in queue
input image full path|param file full path|output image full path|file format|jpeg quality|jpeg subsampling|png bit depth|png compression|tiff bit depth|tiff is float|uncompressed tiff|save output params|force format options|fast export|
I never tested a queue with ten thousands of files, so it may happen that rt starts very slowly with such a queue file.
Another way would be to write a script which calls rawtherapee-cli for every file in every folder.