In Sonar, there is Now marker and Now time line. When transport is stopped, they both point to the same time. When transport is moving (f.e. in play), Now marker is not changed but Now time is moving. When pause is engaged, Now marker is still not changed but transport is stopped without Now time return to sync with Now marker.
When transport is stopped, Now marker and Now time are synced again. The option "On Stop, rewind to Now Marker" controls how. If that option is set, Now time returns to Now marker. When the option is not set, Now Marker is moved to Now time (so the option name is a bit misleading).
Commands:
"Play/Pause" does pause for me (when playing)
"Stop" (or "Play/Stop") stop transport according to "On Stop, rewind to Now Marker" option
"Stop With Now Marker" stop transport moving Now Marker to Now time, independent from the option.
All these commands can be used in AZ Controller, and there is yet another way (I must admit I have not used it so far, but it is there):
Action "Function" / Transport / Pause On/Off/Toggle.
My guess that is precisely what transport buttons in Sonar toolbar do, while key bindings use mentioned commands.