2.4 If two files with the same name exist, one in the temporary domain and one in the permanent domain, it appears that FINFO will operate on the temporary domain file. Is this generally true for CI commands and functions?

Yes. Which means you can get into trouble if you are not careful since you may think you are working with a permanent domain file, but in fact are working with a temporary domain file. Then you sign off and, poof, there goes all your work. Because temporary domain files in MPE are really that, temporary, and last only as long as the session or job.