Blimey!
... I did some more testing. Using the TOSEC supplied script to create the directory structure, move the files into the appropriate directories and copy to the CMP datfile folder of a fresh CMP v4.031c installation produced the following results:
a) Datfile: 3DO 3DO Interactive Multiplayer - Applications (TOSEC-v2012-07-05)
Datfile name tag: <name>3DO 3DO Interactive Multiplayer - Applications</name>
Datfile path: <cmproot>\datfiles\TOSEC-ISO\3DO\3DO Interactive Multiplayer\Applications
Using rompath naming "DatFile Name Tag" the rompath became:
<rompath root>\TOSEC-ISO\3DO\3DO Interactive Multiplayer\Applications\3DO 3DO Interactive Multiplayer - Applications
Er... what? Oh yeah, user error, I didn't want to use the 'datfile name tag' option, let's try again with the next file

b) Datfile: 3DO 3DO Interactive Multiplayer - Bonus Discs (TOSEC-v2012-07-05)
Datfile name tag: <name>3DO 3DO Interactive Multiplayer - Bonus Discs</name>
Datfile path: <cmproot>\datfiles\TOSEC-ISO\3DO\3DO Interactive Multiplayer\Bonus Discs
Using "DatFile Folder" option, the rompath became:
<rompath root>\TOSEC-ISO\3DO\3DO Interactive Multiplayer\Bonus Discs\Bonus Discs
Looks goo... WAIT!?! What? Why did the end element of the path double?

*sigh* Does that mean I actually may be able to move the actual datfiles up one level in the datfiles folder?
Try again moving the rest of the datfiles in the datfiles directory up one level ..
c) Datfile: 3DO 3DO Interactive Multiplayer - Educational (TOSEC-v2012-07-05_CM).dat
Datfile name tag: <name>3DO 3DO Interactive Multiplayer - Educational</name>
Datfile path: <cmproot>\datfiles\TOSEC-ISO\3DO\3DO Interactive Multiplayer\
Using "DatFile Folder" option, the rompath became:
<rompath root>\TOSEC-ISO\3DO\3DO Interactive Multiplayer\3DO Interactive Multiplayer
Ooookay ... from the previous try I kinda expected that. Use the datfile path and double the last element

d) Datfile: 3DO 3DO Interactive Multiplayer - Firmware (TOSEC-v2012-07-05_CM).dat
Datfile name tag: <name>3DO 3DO Interactive Multiplayer - Firmware</name>
Datfile path: <cmproot>\datfiles\TOSEC-ISO\3DO\3DO Interactive Multiplayer\
Using "DatFile Name Tag" option, the rompath became:
<rompath root>\TOSEC-ISO\3DO\3DO Interactive Multiplayer\3DO 3DO Interactive Multiplayer - Firmware
Kinda what I expected from a) but still not what I was looking for

So... am I doing something wrong, or is it the naming function? I was expecting was to get somehow to:
<rompath root>\TOSEC-ISO\3DO\3DO Interactive Multiplayer\Applications
<rompath root>\TOSEC-ISO\3DO\3DO Interactive Multiplayer\Bonus Discs
<rompath root>\TOSEC-ISO\3DO\3DO Interactive Multiplayer\Educational
<rompath root>\TOSEC-ISO\3DO\3DO Interactive Multiplayer\Firmware
And the associated DatFiles located at:
<cmproot>\datfiles\TOSEC-ISO\3DO\3DO Interactive Multiplayer
Note: The directories where the roms should go were also already in place before I loaded the dat files.
Any idea?