Just in case anyone's interested, I've refined my workflow for this a little to reduce the amount of clicking required.
1. Open Handbrake's preferences pane, and in the general tab configure it to send the output file to Subler on completion.
2. Use MakeMkV to rip your TV show DVD. Output the files into one folder per disk, with the files named as per my post above (you'll need to enable "advanced" in the MakeMkV GUI to set the file name).
You should end up with something like:
/Users/Jim.R/MKVS/SEINFELD_S1_D1/Seinfeld S1 E1.mkv
/Users/Jim.R/MKVS/SEINFELD_S1_D1/Seinfeld S1 E2.mkv
etc...
3. Once the all the titles have ripped, go to Handbrake and click "Open source" and select the folder created above (not the individual files). This will open all of the files in that folder as separate titles.
4. Select the pre-set you want to use, make any other modifications and then click "File" > "Add all titles to queue".
5. Open the queue window and hit Start.
Now, while that runs, repeat steps 2-4 for the other disk(s) in the set to add them to the Handbrake queue. Again, make sure each disk is ripped to a separate folder (e.g. the next disk would rip to "/Users/Jim.R/MKVS/SEINFELD_S1_D2"
As Handbrake finishes encoding each episode, it'll now automatically open the MP4/M4V in Subler for you to add metadata.