By Rule 7B the department gets more time period to issue SCN for recovery of ST not paid/short paid. Naturally the department will prefer this rule.
Whenever there is a clash between the Act and Rule, the Act will prevail over the Rule. In Central Excise era, in one of the cases (Compounded Levy Scheme), penalties were imposed upon a large number of assessees under Rule but there was no statutory provision for imposition of penalty under Central Excise Act. All penalties were set aside by the Supreme Court and the department accepted that order of the Supreme Court.