Comment 3 for bug 1515426

For your information, Alitum Designer (15.1) default setting is to use only one file. It add ";TYPE=PLATED" or ";TYPE=NON_PLATED" before the tool definition list of each kind.

Example of a single drill file (generated by Altium) with one plated hole and two non_plated holes (with different size) :

M48
;Layer_Color=9474304
;FILE_FORMAT=2:5
INCH,LZ
;TYPE=PLATED
T1F00S00C0.02800
;TYPE=NON_PLATED
T2F00S00C0.02800
T3F00S00C0.03200
%
T01
X017Y025
T02
X016Y027
T03
X018Y027
M30

I have not access to other CAD software, but at least it gives you one way to define the drill type.