How do I update Drupal 8.2.3 REST configurations for an entity?
To answer your second question, you'll want to remove the imported configuration from the database and then reimport it with an included UUID - after which you can overwrite the config by re-importing it as many times as you like.

But first, when you upload a config, you should give it a more meaningful ID; rather than 'entity.node', you want something like 'my_config_for_this_thing'.

So in steps:


In your DB, find the config you uploaded (and see note about about the config ID):

select name from config where name like '%entity.node%';

Copy the full name that matches your config.  It will be something like 'migrate_plus.migration.entity.node'.
Delete that row from the database

delete from config where name = '*paste that name here*';

In your yml file, include a uuid. You can generate one locally or using a web tool such as https://www.uuidgenerator.net.  This will look something like

id: some_meaningful_identifier
label: 'A label to describe my config'
status: true
uuid: ac1d69cc-382f-49d2-921e-bb0673fd62ea

Clear your Drupal cache
Then re-import and you should be in better shape.