The provision of TCS says that.
Section 206C(1H): Section 206C(1H) – Every person, being a seller, who receives any amount as consideration for the sale of any goods of the value or aggregate of such value exceeding fifty lakh rupees in any previous year at the time of receipt of such amount, collect from the buyer, a sum equal to 0.1% of the sale consideration exceeding fifty lakh rupees as income-tax.
Hence the TCS is on receipt of amount so it is calculated on total amount received i.e including GST.
For ease of documentation and collection every one is doing in invoice itself
Hence TCS is not part of invoice so it should not be reflected in E invoice i.e it should not be added in GSTR 1