I've written a number of blog posts about Stock Submitter and how I use it (that you can find here:
https://www.backyardsilver.com/?s=stock+submitter)
I have used it now for about 2 years and find it essential to support my uploads to about 16 agencies. I don't upload as many as you - more like 100 - 400 a month, but I don't see the issues you are reporting. I also don't do as many model releases either, so that might play into my experience.
Yes, there are issues sometimes with some agencies, but if I come back to those agencies after a few days, I find that the App has been updated and the issue has been fixed. Because it remembers which images have been successfully uploaded, it is easy to just select a bunch and let the system decide which ones need to be uploaded to an agency that was missed before.
I can't imagine how difficult it is to keep an app like this up to date as agencies change their page designs, but I think the developer does a good job at it.
Steve