The LTI configuration links to a single, specific MyOpenMath course.
So, if the “account level” is used, then all Canvas courses using the LTI will link to the same MOM course. This would be helpful if you wanted multiple Canvas courses to share the same MOM resource (eg, all Intermediate Algebra sections use the same master-MOM course). However, any changes to the LTI settings (for example, changing the MOM reference course) will impact all Canvas courses with that LTI.
If the LTI is setup at the “course level”, then individual Canvas courses can link to different MOM courses. This would be helpful if individual courses wanted to link to different MOM resources.
I prefer the latter, which is to setup the LTI at the course level. It's more work to setup each course, but those courses maintain independence with regard to the parent MOM course.