The “traditionally the Clans have better skills for their mechwarriors” is reflected in the higher chance of being Elite/Heroic. It does not make, in BattleForce, an Elite Clan Mechwarrior better than an Elite Inner Sphere Mechwarrior.
Total Warfare and then converting to BattleForce: Total Warfare defines a range (1-2 4/3, 3-4 3/2, 5-6 2/1) not a specific value to being Elite. Clan Mechwarriors do get a +1 to each roll (piloting and gunnery), but that’s only a 50% chance of bumping up each. The “odd” skill bump is lost in converting to BattleForce (3/2, 3/1 and 2/2 are all a total 4-5, which is a 2).
Directly generating BF skills: SO p321 generates an BattleForce skill level and gives a +1 to the roll, but that just increases the chance that a Clan Mechwarrior is Elite (2), or Heroic (1). It doesn’t change the definition of Elite. An Elite is always a 2. A Clan Mechwarrior is just more likely to be Elite (and/or Heroic) than an Inner Sphere Mechwarrior, but a Clan Elite Mechwarrior and an Inner Sphere Elite Mechwarrior are both a 2.