"Guarding the controls below MSA" that a poorly written SOP in my opinion.
Sometimes MSA is 14000 feet sometimes it's 1800. If it's 1800, why shouldn't you guard the controls at 2000 feet. (Don't answer because the SOP says so).
Our SOP say with flaps extended, which makes sense because a) you started to configure which makes it easier to take over in case of flap asymmetry, and b) it provides a fairly equal height above terrain where the controls are covered.
Personally I guard the controls when ever I am getting ready to "fly" the aircraft. Which means about 10000 feet AFE.