SQL Server 2016 SP1 Replication: creation of publication stops with nvarchar(max) not supported with memory optimized tables
Fixed it. The @schema_option shouldn't be  0x40000000000 but 0x80000000000. This means the replication converts clustered index to nonclustered index for memory-optimized articles. It's nowhere close to error message. 

So, if you need to create a replication from a disk table to a memory optimized table, do not let the wizard do the work but create the script en alter the @schema_option. 
At least this lets you create the publication and the subscriber can connect to the publication.

Bugger, not fixed. Yes, the creation of the entire replication procedure works great. But then, the new memory optimized tables do not get created. The only thing this stupid feature does is drop the table (whether they exist or not). And then starts complaining the target table does not exist. 

Now trying to hack the @schema_option to combine the 0x40000000000 and 0x80000000000. Somehow these values cross a threshold that makes them readable to SQL Server. One or the other works (and results in failures or weird behavior) together nothing...

Still not working in version 17.1 of Management Studio.

-- edit november 2017

The newer versions of Management Studio seem to support the in-memory to in-memory replication. And the error handling has improved. 
So question marked as solved. If anyone still encounters issues, please add to this question :)