You are definitely correct that we would not make back 5 stops worth of time by switching to EMU, and that it is theoretically possible to build a DMU that accelerates as quickly as an EMU at low speeds. However the DMU scenario is not a theoretical DMU, it is the Nippon Sharyo DMUs the original 25-minute schedule was based on. Those diesel-mechanical units accelerate very slowly because the engine is rarely at the optimal rpm, they need to pause while changing gears, and at the time there was a 10 mph speed restriction at platforms.
Based on my measurements, UP Express trains used to take about 70-80 seconds to reach 100 km/h.
Some of the 10 mph restrictions have recently been lifted so I'm planning to take some new measurements over the holidays to see how much acceleration has improved.
European EMUs typically take about 30-40 seconds to reach 100 km/h. They only take 24 seconds to reach 40 mph (64 km/h) so with similar EMUs the UPX would spend nearly all of its moving time above 40 mph.