nightly-ci: Run tests as part of script section

pytests inside the nightly jobs `sw-vsi-config-test`,
and `gnu-toolchain-test` should be run as part of the
`script` section of these jobs as running the tests
in the `after_script` section of these jobs won't
have an influence on the exit code of the pipeline
which might lead to false negative misleading CI results.

Signed-off-by: Ahmed Ismail <Ahmed.Ismail@arm.com>