I'd suggest keeping the lower cost. People don't really use tinkers all that much in recent builds.

Either cost calculation from components and recipes table should be consistent, or recipes table phased out for components altogether.

I am not opposed to costs calculated from Recipes table to prevent player from stockpiling tons of damaged components for the few items it is effective for (dual turbolaser from the turbolasers from numerous Viking wrecks). It was huge income source when all Custom Work used to cost only 50 credits many versions ago. However, the current way discourages people from using functional items as components, and (maybe) aside from dual mark III or omni x-ray laser, that is a bad trade.

I do not use Custom Work much (when playing) because the components for most things are too hard to get when I want the item, and when I find the components, the item is obsolete. Also, many of the items have junk enhancements that inflate the cost too much.

Currently the new Components system only supports the new pricing scheme - where crafting cost is markUp * component cost (markUp is 1.25 for armor, 1.5 for devices, 1.2 otherwise)

The recipe system supports three methods: tinker pricing (difference between the final item price and the component cost), component markUp, and totalCost.

For details see Crafting Reference, Request: Allow overriding the automatic cost-calculation in Tinker craft recipes and Tinker Updates

From Tinker Updates:

Do we need to enhance the component crafting code to support some of the Tinker recipe features (like fixed prices, etc.)?

Yes, we'll probably want some of the Tinker features ported to the new system.

I was also considering extending the Tinker recipe system to let it 'wrap' crafting recipes so you could allow enhancements / fixed prices, or ways of controling when recipies are available etc.
e.g. a tinker recipe with:{ item:&itOrthoSteel; enhancement:"+regen" components: ( 'craftingComponents { item:&itDuralloyOre; count:4 }) }
could allow you to craft an enhancemt segment of armor using the default components for that armor + dualloy ore

this would also allow you to have variations of the same recipe from multiple sources. e.g.
Corporate might craft the recipe at 0 markup for players with high rank.
Tinkers have the same recipe for everyone, but at high cost.