Transport Allowance and Medical Allowance has been paid as fixed allowance apart from the Basic Salary all these years as they were non-taxable. However, they were part of Gross Salary and CTC.
Now that these two are taxable, one option is to continue paying the two allowances in the same manner as before, in which case the two will be added to taxable income; the other is to add the two allowances to the Basic, in which case they come under all other calculations which are based on Basic, eg. HRA, PF, etc. Also, once you increase the Basic by adding these two allowances to the previous Basic, it will be difficult to reduce the Basic at a later stage if this amendment is reversed by some future govt.
Best option is to continue paying the two allowances as it is and add it to Taxable income.