Well, by stacking chk damage high you will obviously improve the % jewels. I played with my excel and I actually can get closer to both jewels being equal than I thought.
In my case of a pve whipper with a crit weapon, non-hp Bangle, Eta gloves and all Wizard/Ghost accessories (trinket is only rare) i have a base min/max chk damage of 1324/1901 including 45/46 for being level 65. Min/max % is 14% from pet chip and earrings.
So in my character stats I see 1324*1.14=1509 min and 1901*1.14=2167 max.
You can easily see what happens if you add flat 16 here or 2.4% there. Just looking at the max stat:
1917*1.14 = 2185 with 1 rank 2 chk atk jewel
1901*1.164 = 2213 with 1 rank 2 chk atk % jewel
% jewel shows higher value in character stats
But I am not attacking with a 100% attack. Checking the stats sheet, the rank 8 Electric Tempest has a 400% multiplier (and conveniently for keeping it simple no bonus damage). So instead of multiplying 1.14 we multiply 4.14.
1324*4.14 = 5217 min damage
1340*4.14 = 5548 with 1 rank 2 chk atk jewel
1324*4.164 = 5513 with 1 rank 2 chk atk % jewel
1901*4.14 = 7870 max damage
1917*4.14 = 7936 with 1 rank 2 chk atk jewel
1901*4.164 = 7916 with 1 rank 2 chk atk % jewel
You can see, the % jewel scales with your base damage, the flat damage jewel scales with your attack skills, more precisely their multiplier.
I my case, attacks that have a multiplier of around 280 will have both jewels about same. But most of the attacks that matter, also looking at mech, have 300 or more.
For other classes it's probably completely different. Can't be bothered to calculate that.