Hi phuntz, maybe we can work through some of this together since I am also dealing with 3rd type boundary conditions for a river at the moment and have been doing quite a bit of research into the fairly sparse Feflow documentation.
Hopefully DHI will come back and help us with some of this however.
-Considering your stream/ditch is ephemeral (dries up), and overlies clay, is it necessary to assign boundary conditions to it? It seem it would not contribute significantly to recharge or discharge and mostly just handle runoff. Especially if the ditch was lined with some form of membrane or geotextile.
-Have you seen that the Fluid transfer BC has limiting conditions available that can be set to avoid to much (unrealistic) loss or gain into the ditch? Modflow handles this automatically by not letting the head go below the stream bottom by default. However in Feflow it seems we need to set this manually. DHI, please correct me if I am wrong.
I will try and provide additional info if I come across anything new. I know this is not much help and not a definitive answer, but maybe it will spark some thought to help us solve your problem. I will also keep an eye out for definition of D for you, but suspect it has something to do with thickness since that is what D is frequently used for if I recall.
Cheers,
Drake