SQL Server & SSDT : Error modeling database during Publish after adding CREATE AGGREGATE / EXTERNAL NAME
I can't reproduce this problem using the same version of SSDT as you.  I do have a slightly newer Visual Studio (15.9.24), but I'd be surprised if that matters.  Here's my (very minimal) setup, please let me know if I've misunderstood some part of your scenario:
SSDT Project

clr.sql
CREATE SCHEMA [clr]

Stats.sql
CREATE SCHEMA [Stats]

StatsEntropy.cs
using System;
using System.Data.SqlTypes;
using Microsoft.SqlServer.Server;

[Serializable]
[SqlUserDefinedAggregate(Format.Native)]
public struct StatsEntropy
{
    public void Init()
    {
        // Put your code here
    }

    public void Accumulate(SqlString Value)
    {
        // Put your code here
    }

    public void Merge(StatsEntropy Group)
    {
        // Put your code here
    }

    public SqlString Terminate()
    {
        // Put your code here
        return new SqlString(string.Empty);
    }

    // This is a place-holder member field
    public int _var1;
}

Default Schema

Normally that failure during preview generation indicates that there are objects in your target database that don't exist in the SSDT model (dacpac).  That's discussed on Stack Overflow here: SSDT Publish errors on Creating Publish Preview
You can use the &quot;Schema Compare&quot; feature to check and see if that's the case for you.
If there are no conflicting objects in the target, then it would be helpful if you could edit your question to include your publish settings (the &quot;.publish.xml&quot; file, or at least screenshots of the &quot;Advanced&quot; window when publishing).  It could be some odd combination of options causing the problem.