I have tested the Custom Tools plugin to (automatically) installing a zip- or tar.gz archive; which works fine.

Assuming, that is it possible to overrride the tool-location, I have configured and (alternative) Home (in Configure System -> Tool Locations).
The previously configured tool (eg. "gcc-4.9.2-i386") is listed in the drop-down box as "(Custom Tool) gcc-4.9.2-i386"; but the configured folder isn't used (in the job-run).
The archive is still installed/unpacked in the default-directory
(Ie. "C:\..\Jenkins\tools\com.cloudbees.jenkins.plugins.customtools.CustomTool\gcc-4.9.2-i386").

Best regards from Salzburg,
Markus