Actually when you will have say, 4k PATK at level 500, any of your skills will deal 8k damage at least due to attributes. That’s where % damage is applied.
And lots of early ranks skills have multihits which is basically {number of hits}*200% scaling. Those flat damages on musketeer skills are sure great, but it basically has only 200-400% scalings, which is LOWER then those early game “low” damage multihits. But I agree, if they fix defense system, then those multihits may become trash one day, but I don’t see it happening in nearest future.
Anyway, musketeer shots are easily blocked by low level priest, so why even care?
And about R6 c2 vs R7, Doppel and Fencer c2 are totally comparable to Dragoon. The same for mages. Cleric and Archer r7 are truly strong, but it’s more about r5-6 classes being weak, basically r2-r3 classes are usually better then r5-r6. I can totally compare c4 chaplain with plague doctor and it is not much weaker (stone skin rules).
That’s why you are free to choose any combination you want, some of them are scaling better and some worse, but there are nearly no truly bad combinations. If you are thinking about your choices cleverly you will never have really big problems with your build.