[test] Use -passes in more Transforms tests

Another step towards getting rid of dependencies to the legacy
pass manager.

Primary change here is to just do -passes=foo instead of -foo in
simple situations (when running a single transform pass). But also
updated a few test running multiple passes.

Also removed some "duplicated" RUN lines in a few tests that where
using both -foo and -passes=foo syntax. No need to do the same kind
of testing twice.