I would like to install a package with a security profile that does not have access to /tmp , but has its own temporary directory, for example /tmp/jeroen         
        
The correct answer was given by @hadley in the comments: in order to make sure install.packages uses the custom temporary directory, one needs to do
Sys.setenv(TMPDIR="/tmp/jeroen")
in addition to:
configure.vars="TMPDIR=/tmp/jeroen"
This way both the extraction and the installation of the package avoids the system or user default temporary directory.