Is it permissible for a sales representative to exploit the transportation expenses clause to achieve financial gain by taking cheaper transportation or obtaining a monthly pass, while charging the company a higher cost?

It is not permissible to take anything from the transport fare difference unless the company gives permission. Otherwise, it would be taking others' money unjustly, which is forbidden by the Quran in the verse: (And do not consume your properties among yourselves through falsehood). Furthermore, this act is considered a betrayal of trust, and Allah and His Messenger have forbidden treachery. Allah says: (O you who have believed, do not betray Allah and the Messenger or betray your trusts while you know). And the Prophet, peace and blessings be upon him, said: "Render the trust to the one who entrusted you, and do not betray the one who betrayed you."