The systems are built with multiple layers of bonus logic, stats, race, ranks, profession, etc. This is intended IMO to create more variation in results.
The odds on two characters having identical bonuses in multiple skills gets lower every time a new factor is added.
The professional bonus itself, is intended to reflect central core concepts of a character's ongoing routine. . .fighters fight, they think about fighting, they train in fighting, they talk about fighting with their friends, they watch fighting carefully and notice details they can use. This focus on fighting gives them a fighting bonus.
Game balance issues wise, in the majority of instances, the professional bonus remains the minority of the total bonus. (The closest to absurd is the 20th level RM2 fighter with 1 rank in flail who has +5 skill bonus, and +60 professional bonus). But that's not a balance issue in terms of the other players, since likely the same fighter has their primary weapons out into the +150 or better range, so that sub +100 total bonus in flail isn't making them step on the toes of the other players.
The fact the fighter is say 10-30 bonus ahead of the rogue, even in the rogue's primary weapon, is balanced by the fact the rogue does non fighting stuff better.