No, because in this analogy, it matters not whether the line is grade separated or not - you are still slowing way down from the previous track speed.
Hell, you don't need to even look at slow zones - in between Bloor-Yonge and Eglinton West, Line 1 naturally slows way down due to shorter distances between stations, and the presence of many curves and timers. But you don't see a traffic jam outside those 2 stations going southbound, because, if the line is running according to plan, *every single train* starts equally fast and then slows down to the same rate of speed.
Bottom line is this: as long as all trains are operating under the same conditions, are all subject to the same speed limits and operating rules, there is zero reason why bunching should occur.
Bunching happens due to random acts of chance that develop during the day: passengers that take their time getting on, disruptions such as door holders, alarms, minor mechanical problems, an inability of terminals to process the correct amount of trains in one go (this is why there is routinely bunching outside of Finch and Kennedy during the rush hours), and on the surface network, the irregularity of mixed traffic, and operators playing games (i.e. they cling to their leader's ass, so that they don't have to pick anyone up and can have an easy trip). Having a line with mixed top speeds is not at all a factor.