I would like for atlas to consume ink sack or any specified item in config if possible in configurable rate while generating each chunk in atlas.

Sounds like a nice improvement to me, but I wouldn't see the costs that high. One inc sack per chunk sounds excessive to me.

A broader option would be to implement something like an inkwell that you fill up with ink from the ink sacks.

In this manner there'd be a pool or basin with x millibuckets of ink, with each chunk using up y millibuckets and ink sacks restoring z millibuckets. If x, y and z are configurable then users and pack makers could balance the way they see fit.

Sounds good to me.

ideally, the inkwell would be in the map gui rather than another item that needs to be kept in inventory.

This is an interesting mechanic. Personally, I wouldn't use it in fear of ink running out at the most inopportune moment, but we could make it a configurable option.

would that work with thaumcraft's scribing tools? they use roughly the same mechanic so me likey

Each ink sack could work for some chunks (configurable). Looks pretty good and non-op to me.