Need to add `pbench-init/end-tools` calls in other benchmarks

[portante]

While we merged the persistent tools work (PR #1824), we overlooked one important task that remained: adding calls to pbench-init-tools and pbench-end-tools in other benchmarks besides pbench-user-benchmark (see lines 304 and 340) and pbench-run-benchmark (see lines 302 and 397).

[portante]

Implemented with #1862.