But I see nothing that tells it whether to grow the primary MDF, or grow by adding additional NDFs.
There is NO option native in SQL Server that will allow you to do this, unless you explicitly specify to add additional secondary files (.ndf) using Alter database command.
More info Files and Filegroups Architecture & Database Files and Filegroups.
Is there a way to combine these NDF files back into the primary MDF?
DBCC SHRINKFILE ('ndf-secondary-file-name', EMPTYFILE)
Note: You can move data from one FILEGROUP to another FILEGROUP. But if it is same filegroup, then SQL Server will manage where the data goes when you have multiple files in the same filegroup using PROPORTIONAL FILL algorithm (i.e. allocating the extent from the file that has the most free space).
Now when you have secondary file belonging to different filegroup, then what ?
Now to move a table with a cluster index to a new file group, use ALTER TABLE and specify the file group name that should host the cluster index. Then issue a REBUILD INDEX and the rebuilt index will be created in the new file group. To move a table without a cluster index, the simplest option is to define a cluster index on the table for the duration of the move and then drop it after the move is complete.
If you are curious as to what tables and Indexes belong to what file group and their physical location, then use below query :
idx.name as IndexName
,object_name(idx.id) as TableName
,fil.name as FileGroup
,dbf.physical_name as PhysicalFileName
from sys.tables tb
inner join sys.sysindexes idx
on idx.id = tb.object_id
and tb.type = 'U' and idx.name is not null
inner join sys.filegroups fil
on fil.data_space_id = idx.groupid
inner join sys.database_files dbf
on fil.data_space_id = dbf.data_space_id
inner join sys.data_spaces dsp
on fil.data_space_id = dsp.data_space_id