The purpose of Set Measure/Beat At now is to change the M:B:T timeline relative to absolute time without affecting the absolute playback timing of either audio or MIDI for the purpose of aligning the timeline to a existing MIDI/Audio. That's why MIDI doesn't follow the tempo change.
When you SM/BAN, SONAR calculates the tempo needed to make the specified beat fall on the current Now time, and re-calculates MIDI start times and durations to preserve their absolute playback timing at the new tempo. The most recent tempo is changed, and a new tempo of the same value is inserted at the Now time as a reference point for setting additional points further out in the timeline if needed.
Using SM/BAN is the only way to make tempo changes without altering the absolute playback timing of MIDI. MIDI will follow any manual tempo change you make. You can use SM/BAN to restore the original tempo starting at the point you set by the following method:
- Set the Now time at the measure corresponding to Current Tempo + 2 (i.e. 362 in your example)
- Shift+N, enter Target Tempo + 2 as the Measure, and OK.
SONAR will recalculate the tempo at 2:01:000, returning it to the original tempo without changing the playback timing. So now you'll have the high tempo only for the first measure to align the video.