I think most are overestimating it
MTTs have some history of big, game-changing differences, especially close to the end of the race. Way bigger than normal stages in those races. PDBF TT (we know it well), Alpe'04 (where Armstrong and Basso were inseparable earlier), Abantos'03 (Vuelta, where Heras put into Nozal way more time than in previous stages). I do think that even between closely matched rivals a gap can occur: form fluctuates every day and normally a small gap of form between riders can be hidden by tactics (too late attacks, short time of an all out effort) and by riding on a wheel. Here there's no hiding, you push maximum all the time. And 29 seconds is really not a lot on such a monstrous TT, even if Thomas is only somewhat weaker than Roglic a gap like that can happen.