OK, this is where it was getting complicated but re-re-re-reading the two readmes has finally got me there!
For the sake of anyone else who might want to try this, these are the two extra steps I had to do.
Having set custom directories for Locus and having set Locus root to my secondary SD card, I had to
1. Edit storageconfig.txt in the brouter/segment3 folder to have the line:
(And then remember to remove the # at the start of that line). That's the value I had chosen for the Locus root directory
2. In /storage/sdcard1/Android/data/menion.android.locus.pro/files/Locus/mapItems, where BRouter attempts and fails to write a track (construct that location from the result in step 1) I had to create a text file named brouter.redirect with a single line that is the location where I wanted the track to be written, such as /storage/sdcard1/brouter (or in my case, /storage/sdcard1/LocusMaps/mapItems, which was the value I had set for my my custom writeable mapItems folder)