sim: testsuite: rework sim_init usage

The sim_init function was called by runtest for each test when --tool
was set to sim.  When we changed to --tool '' to collapse the testsuite
dir, the init function was no longer called on every test.  However, it
was still being called explicitly by config/default.exp.  It's not clear
why that explicit call ever existed since, in the past, it meant it was
redundant.

Lets drop the single sim_init call in config/default.exp and move it out
to all our tests.  This replicates the runtest behavior so we can setup
variables on a per-test basis which allows us to recollapse the sim_path
logic back.  We'll also leverage this in the future for toolchain setup.

Also add a few comments clarifying the overall runtime behavior.

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