Regarding Transportation Allowance

Yes. Correct.

1. From the FY 2018-19 Transport (conveyance ) allowance and medical reimbursements were substituted by Standard deductions u/s 16(ia).
2. Hence, the exemption in relation to the above allowances is no longer available to Individual.
3. From the FY 2018-19, transport allowance and medical allowances will form part of your salary and standard deduction of Rs. 40,000 alone will be deducted from your salary. 
Please correct me if the above solution has an alternative view.