Can I specify public: '../src/main/webapp' as a path in config.coffee and safely use brunch without fear that it will delete content from src/main/webapp?
yes
Can I leave my Thymeleaf templates in WEB-INF/web-templates?
yes
Is there any other points to take into account?
I would suggest making "webapp" 100% auto-generated so that you could delete it freely. Also, to not keep generated stuff in repository.
This can be accomplished by moving all your stuff to app/assets
directory, for example. Things from assets
directories are copied as-is to public
directory. But it's up to you.