Two bids for the same trade rarely cover the same work. The general contractor lists the scope items, marks what each bidder included and adds a cost for each gap.
Example: one flooring bid includes floor prep and one excludes it. The estimator adds a prep cost to the second bid before comparing the totals.
A clear proposal levels well. List inclusions and exclusions in plain words and match the spec sections by number. If the estimator has to guess, the estimator adds money to your number or sets your bid aside.