Different instructors learned from different schools and have different standard operating procedures. An experienced instructor will probably tolerate more differences than a new one who only knows one way, but we all have an obligation to point out practices that may be unsafe.
For example, why not raise the flaps on the runway? If after 400 hours you cannot physically prevent your right hand from flicking up the little gray lever on the dashboard as soon as your wheels are down, please don't fly a Beechcraft Duchess. That lever is the gear retract.
If an operator gives me an SOP that I consider safe, legal, and moral, I will do my utmost to follow it. After all, when I'm in a plane I should be thinking about what I'm doing, not just mindlessly doing it.