If a contract contains limits on allowable travel costs, regulations for contractor travel and transportation allowances are usually based on Part 31 of the Federal Acquisition Regulation, which relies in large part on each contractor's own travel rules, or a contract clause that addresses travel costs. The contractor should speak with the Contracting Officer or Contracting Officer Representative for rules that apply to the individual contract.
No, the JTR does not apply to contractors. The JTR was written for and only applies to civilian employees of the Department of Defense and the Uniformed Services.
Any travel rates offered by transportation carriers, negotiated by the Government for Service members or civilian employees do not apply to contractors. Commercial car or hotel vendors may voluntarily offer discounted rates for contractors at their discretion or contractors may negotiate rates for their employees with the carrier, hotel, or rental car vendor.