Some of the "passthrough tests" in our javascript testing framework work by setting some global configuration that gets checked by all the shell helpers that spawn new programs.

For example, running smoke.py with --use-ssl, will use the "--eval" in the mongo shell to set some global configuration that signals to all the shell helpers to spawn programs with ssl options.

You can see an example of a place where this configuration is checked here: https://github.com/mongodb/mongo/blob/r2.6.0-rc0/src/mongo/shell/servers.js#L421

However, the two helpers for spawning "tools" from the mongo shell for the purposes of jstests ignore this configuration, which means the tools to not benefit from the extra test coverage in the passthrough testing:
https://github.com/mongodb/mongo/blob/r2.6.0-rc0/src/mongo/shell/servers.js#L702
https://github.com/mongodb/mongo/blob/r2.6.0-rc0/src/mongo/shell/servers_misc.js#L58