Migration scripts (and hence the /migrationfolder option) require you to use SQL Source Control in conjunction with SQL Compare (command line or UI) so this isn't an option for you. SQL Compare cannot leverage migrations scripts without the migrations repository created by SQL Source Control.
If you want to read more about how this works, please visit the following link:
http://www.red-gate.com/supportcenter/c ... Migrations
I'm still struggling to understand why you can't use sqlcompare.exe /project. This only uses the UI once to create the project that includes the table mappings. After this you can just use the command line and reference the project. Is there any reason why you can't create the project?