A criticism of Discovery's ship scales assumes too much if it treats the Enterprise-D as necessarily the fleet's largest vessel. A battleship may be the principal combatant while an aircraft carrier, assault carrier or freighter is larger. An exploration navy could sensibly put its flag aboard a medium or upper-medium cruiser. That cruiser might exceed many other ships in size while remaining smaller than battleships and other large vessels.
Notable Point · 3:38:43-3:39:39
Why a flagship need not be the fleet's largest ship
Command status and combat importance do not determine hull size: a cruiser can carry the flag while carriers, freighters or battleships are larger.