usage percentage of Mongodb internal cache
What could have caused the difference in the cache percentage usage and throughput?
MongoDB uses both file system as well as WiredTiger's cache when required 
Is it safe to change explicitly this settings so Mongodb uses more of its cache?
Yes. It is totally safe to change the cache settings
Can I do this setting change from the command line ? 
The setting has be done in your mongod config file under storage option


Refer the below link on how you should decide on the cache size
https://docs.mongodb.com/manual/faq/storage/

Similar to the below:

storage:
  engine: wiredTiger
  wiredTiger:
    engineConfig:
      cacheSizeGB: 7


Thank you!

-Anban