The difference between a custom and non-custom epic armor piece is a total of 20 HPs+MPs (20MP for comms, 5HP and 15MP for enges, 10HP and 10HP for ops.)

That equates to 100HPs+MPs for a full set of 5x customs. (100MP for comms, 25HP and 75MP for enges, 50HP and 50HP for ops.)

It costs 10k + materials to customize, or 50k + materials to customize a full set.

Is it worth it?

I guess if you had a guild that could afford the recipe cost, the prices would go down to just materials...