OK, this is realized now, in the beta version at
http://hgm.nubati.net/WinBoard-TM.zip . I added a new option there:
/singleEngineList true|falseThe compiled-in default is 'false', in which case you will have the old behavior. When you set it to 'true', however, the second combobox will also display the /firstChessProgramNames list, and when you type an engine name there, you would have to type it exactly as you would type it in the first combobox: with /fd=, /fUCI rather than /sd, /sUCI etc. (When you set it to 'true' by typing it in the 'Additional options' field, you are obviously too late to still affect what is in the comboboxes, and the effect on the engine choice is undefined, but as this is a persistent option, the new setting will be in effect next time you start WinBoard.)
The Load Engine and Tournament / Match menu dialogs already use exclusively the first list, and in the Load Engine dialog you have the option to install every engine from that list as frst or second. I already removed the menu item to edit the /secondChessProgramNames list. So I guess in future releases I might configure the -singleEngineList option as 'true', and we can forget completely about the second list.
For specifying engines from the command line, the /fd, /sd, /fUCI, /sUCI etc. options remain as they always were.