When I lived in Brookline Village, I worked at the Federal Reserve Building. I took the D-line to Park, Red line to South Station, door to door averaged 25 minutes. Khata has a longer commute than that, but over much of the same path. He can get the D-line at Reservoir or Beaconsfield, depending on what he means by living near Cleveland Circle. That adds five minutes to my 25 to get to South Station. My experience with the Silver Line has been pretty consistent -- 5 to 10 minutes from South Station to World Trade Center. Let's round things up a bit, we're still talking 45 minutes, an hour if things don't go well. No way is that a 90 minute commute.
Have you calculated Rush hour? Not to mention that he likely have to wait for the arrival of a Green Line train, a Red Line train, and the right Silver Line bus. I was a BU student till quite recently and use the trains a lot in those years. The times I get to Park in 25 minutes are the times start paying attention to the time I get to the station with the train right there and the Red Line already there. I have long found the biggest eater of time is rush hour, walking to/from the station, and waiting for the train. And Kahta have to wait x3. If there's a 10 minute walk to and from the stations, there's 20 minutes already.
Walking to Station: 10 mins.
Waiting at Station: 5 minutes.
Reservoir to Park: 24 minutes (Per google)
Waiting at Station again: 5 minutes:
Park to South: 4 Minutes (Per google)
Waiting at Bus Stop: 5 mins
South to WTC: 8 mins (per Google)
WTC to work: 10 mins
Calculated time: 71 Minutes - 1 Hour and 11 minutes
19 Minutes short, but that's not taking account of Rush Hour, and my experiences is Rush Hour always takes longer than outside of it.
You can argue you wait time is less on average, but I never felt it. I have to wait more than negligible time (like 5 minutes) during rush hour at Kenmore.
You might argue it might not take 10 minutes to walk to the station. I'll ask to time yourself how long it takes sometimes to cross some busy streets. You'll be surprised.
Even if Rush Hour only adds 10 minutes, then it's already 1 Hour and 20 mins. From picking a time to leave from home or arriving to work, time might as well be rounded.
Verdict: Plausible.