Is There Any Way to Edit the Application Configuration JSON from VAF?

If you're creating the properties via the VAF then why not have your MFIdentifiers assigned the alias of the item you're creating?  That way, once the items are created, simply re-resolve the MFIdentifiers and they'll work without any JSON being altered.

So, this alias won't be seen in the configuration JSON?

No.

[DataMember]
[MFPropertyDef]
public MFIdentifier MyProperty { get;set; } = "MyPropertyAlias";

Is there any way to show the mapped alias in configuration? Or any way to edit the configuration directly to assign the alias into the respective field?

The configuration tab shows the configuration that's been explicitly set by the user and saved into NVS.  If the runtime values are different then they are not shown here.

If you want to show some representation of the runtime values then you would need to do so on a VAF dashboard or similar.

Thanks for the answer. Could modify the application configuration through VAF.

Just a similar question here, can we modify metadata card configuration the same way with VAF?

I believe you can do at least some of this.  If you're a partner then take a look at the GPC Developer content from Mexico last year, where we showed using a part of MFiles.VAF.Configuration to interact with configuration.

My personal suggestion would be incredibly careful about this though.  Random VAF applications randomly changing MDCC sounds like a recipe for disaster.