I've responded to a similar topic before, but basically that rule is there to prevent people from gearing alt chars faster than normal. For example if I have a static of 8 people, then we clear 4 floors of the raid on a day, and the next day I bring my alt with my 7 static members and clear the same 4 floors again. If there's no penalty, then I can loot up to 8 gears, 3 upgrade items and one weapon token. Repeat for my 7 static mates' alts (clearing once for each), by the next week our alt group is 8 times as geared as our main group. This would have a very big impact on the early clear race (world first and server first).

Personally I'm not a fan of the loot rules either, but there is a good reason why they're there.