bemi (joint, together). Can that be made into the verbs bemes (join), bemiz (will join), etc?
besi (big). Can that be made into the verb beses (enlarge), besit (will enlarge), etc? Atlas already has vases (grow) but there may be times when enlarge is better than grow. And in Atlas, you can always derive words even if a similar word exists.
Of course! that's precisely one of the big features for Atlas, that all roots can be turned into what you like using the appropiate suffixes!
nires (build). Perhaps "nires" is unnecessary and bines (build) is OK?
"binu" and "nires" come from different ideas. "niru" would be a "construction, building", whatever has been built. So a bridge can be a "niru", or an airport, or a tunnel...
"binu" is a building properly speaking. So every "binu" is a "niru", but not every "niru" is a "binu".
Does it make sense? hope so!